diff --git a/src/gn/build_settings.cc b/src/gn/build_settings.cc
index 6a26495..6d66376 100644
--- a/src/gn/build_settings.cc
+++ b/src/gn/build_settings.cc
@@ -17,6 +17,8 @@
       root_path_utf8_(other.root_path_utf8_),
       secondary_source_path_(other.secondary_source_path_),
       python_path_(other.python_path_),
+      python_path_is_relative_to_build_dir_(
+          other.python_path_is_relative_to_build_dir_),
       ninja_required_version_(other.ninja_required_version_),
       build_config_file_(other.build_config_file_),
       arg_file_template_path_(other.arg_file_template_path_),
@@ -41,6 +43,20 @@
   secondary_source_path_ = GetFullPath(d).NormalizePathSeparatorsTo('/');
 }
 
+void BuildSettings::SetPythonPath(base::FilePath p) {
+  python_path_ = std::move(p);
+  python_path_is_relative_to_build_dir_ = false;
+
+  // If the provided python path is absolute and is within the root source tree,
+  // make it relative to the build directory. This helps keep generated ninja
+  // files free of absolute paths when possible.
+  if (python_path_.IsAbsolute() && root_path_.IsParent(python_path_)) {
+    python_path_ = UTF8ToFilePath(
+        RebasePath(FilePathToUTF8(python_path_), build_dir_, root_path_utf8_));
+    python_path_is_relative_to_build_dir_ = true;
+  }
+}
+
 void BuildSettings::SetBuildDir(const SourceDir& d) {
   build_dir_ = d;
 }
diff --git a/src/gn/build_settings.h b/src/gn/build_settings.h
index e21851a..6c48284 100644
--- a/src/gn/build_settings.h
+++ b/src/gn/build_settings.h
@@ -60,7 +60,10 @@
 
   // Path of the python executable to run scripts with.
   base::FilePath python_path() const { return python_path_; }
-  void set_python_path(const base::FilePath& p) { python_path_ = p; }
+  void SetPythonPath(base::FilePath p);
+  bool python_path_is_relative_to_build_dir() const {
+    return python_path_is_relative_to_build_dir_;
+  }
 
   // Required Ninja version.
   const Version& ninja_required_version() const {
@@ -149,6 +152,7 @@
   std::string root_path_utf8_;
   base::FilePath secondary_source_path_;
   base::FilePath python_path_;
+  bool python_path_is_relative_to_build_dir_ = false;
 
   // See 40045b9 for the reason behind using 1.7.2 as the default version.
   Version ninja_required_version_{1, 7, 2};
diff --git a/src/gn/function_exec_script.cc b/src/gn/function_exec_script.cc
index 6f8bdf5..01cdb66 100644
--- a/src/gn/function_exec_script.cc
+++ b/src/gn/function_exec_script.cc
@@ -182,11 +182,17 @@
   // that the arguments will be passed through exactly as specified.
   cmdline.SetParseSwitches(false);
 
+  base::FilePath startup_dir =
+      build_settings->GetFullPath(build_settings->build_dir());
+
   // If an interpreter path is set, initialize it as the first entry and
   // pass script_path as the first argument. Otherwise, set the
   // program to script_path directly.
-  const base::FilePath& interpreter_path = build_settings->python_path();
+  base::FilePath interpreter_path = build_settings->python_path();
   if (!interpreter_path.empty()) {
+    if (build_settings->python_path_is_relative_to_build_dir()) {
+      interpreter_path = startup_dir.Append(interpreter_path);
+    }
     cmdline.SetProgram(interpreter_path);
     cmdline.AppendArgPath(script_path);
   } else {
@@ -218,8 +224,6 @@
     begin_exec = TicksNow();
   }
 
-  base::FilePath startup_dir =
-      build_settings->GetFullPath(build_settings->build_dir());
   // The first time a build is run, no targets will have been written so the
   // build output directory won't exist. We need to make sure it does before
   // running any scripts with this as its startup directory, although it will
diff --git a/src/gn/invoke_python.cc b/src/gn/invoke_python.cc
index c54ad72..3f5385f 100644
--- a/src/gn/invoke_python.cc
+++ b/src/gn/invoke_python.cc
@@ -20,7 +20,12 @@
                   const base::FilePath& output_path,
                   bool quiet,
                   Err* err) {
-  const base::FilePath& python_path = build_settings->python_path();
+  base::FilePath startup_dir =
+      build_settings->GetFullPath(build_settings->build_dir());
+  base::FilePath python_path = build_settings->python_path();
+  if (build_settings->python_path_is_relative_to_build_dir()) {
+    python_path = startup_dir.Append(python_path);
+  }
   base::CommandLine cmdline(python_path);
   cmdline.AppendArg("--");
   cmdline.AppendArgPath(python_script_path);
@@ -28,8 +33,6 @@
   if (!python_script_extra_args.empty()) {
     cmdline.AppendArg(python_script_extra_args);
   }
-  base::FilePath startup_dir =
-      build_settings->GetFullPath(build_settings->build_dir());
 
   std::string output;
   std::string stderr_output;
diff --git a/src/gn/json_project_writer_unittest.cc b/src/gn/json_project_writer_unittest.cc
index 4b58e2c..770e7cf 100644
--- a/src/gn/json_project_writer_unittest.cc
+++ b/src/gn/json_project_writer_unittest.cc
@@ -36,7 +36,7 @@
   target.action_values().outputs() =
       SubstitutionList::MakeForTest("//out/Debug/output1.out");
 
-  setup.build_settings()->set_python_path(
+  setup.build_settings()->SetPythonPath(
       base::FilePath(FILE_PATH_LITERAL("/usr/bin/python")));
   std::vector<const Target*> targets;
   targets.push_back(&target);
@@ -539,7 +539,7 @@
   target.action_values().outputs() =
       SubstitutionList::MakeForTest("//out/Debug/{{source_name_part}}.out");
 
-  setup.build_settings()->set_python_path(
+  setup.build_settings()->SetPythonPath(
       base::FilePath(FILE_PATH_LITERAL("/usr/bin/python")));
   std::vector<const Target*> targets;
   targets.push_back(&target);
diff --git a/src/gn/ninja_action_target_writer_unittest.cc b/src/gn/ninja_action_target_writer_unittest.cc
index 9b7c76f..8bcea93 100644
--- a/src/gn/ninja_action_target_writer_unittest.cc
+++ b/src/gn/ninja_action_target_writer_unittest.cc
@@ -54,7 +54,7 @@
   target.SetToolchain(setup.toolchain());
   ASSERT_TRUE(target.OnResolved(&err));
 
-  setup.build_settings()->set_python_path(
+  setup.build_settings()->SetPythonPath(
       base::FilePath(FILE_PATH_LITERAL("/usr/bin/python")));
 
   std::ostringstream out;
@@ -96,7 +96,7 @@
   target.SetToolchain(setup.toolchain());
   ASSERT_TRUE(target.OnResolved(&err));
 
-  setup.build_settings()->set_python_path(
+  setup.build_settings()->SetPythonPath(
       base::FilePath(FILE_PATH_LITERAL("/usr/bin/python")));
 
   std::ostringstream out;
@@ -138,7 +138,7 @@
   target.SetToolchain(setup.toolchain());
   ASSERT_TRUE(target.OnResolved(&err));
 
-  setup.build_settings()->set_python_path(
+  setup.build_settings()->SetPythonPath(
       base::FilePath(FILE_PATH_LITERAL("/usr/bin/python")));
 
   std::ostringstream out;
@@ -195,7 +195,7 @@
   target.SetToolchain(setup.toolchain());
   ASSERT_TRUE(target.OnResolved(&err));
 
-  setup.build_settings()->set_python_path(
+  setup.build_settings()->SetPythonPath(
       base::FilePath(FILE_PATH_LITERAL("/usr/bin/python")));
 
   std::ostringstream out;
@@ -266,7 +266,7 @@
   target.SetToolchain(setup.toolchain());
   ASSERT_TRUE(target.OnResolved(&err));
 
-  setup.build_settings()->set_python_path(
+  setup.build_settings()->SetPythonPath(
       base::FilePath(FILE_PATH_LITERAL("/usr/bin/python")));
 
   std::ostringstream out;
@@ -333,7 +333,7 @@
 
   target.config_values().inputs().push_back(SourceFile("//foo/included.txt"));
 
-  setup.build_settings()->set_python_path(
+  setup.build_settings()->SetPythonPath(
       base::FilePath(FILE_PATH_LITERAL("/usr/bin/python")));
   setup.build_settings()->set_ninja_required_version(Version{1, 9, 0});
 
@@ -391,7 +391,7 @@
   target.action_values().outputs() =
       SubstitutionList::MakeForTest("//out/Debug/{{source_name_part}}.out");
 
-  setup.build_settings()->set_python_path(
+  setup.build_settings()->SetPythonPath(
       base::FilePath(FILE_PATH_LITERAL("/usr/bin/python")));
 
   std::ostringstream out;
@@ -449,7 +449,7 @@
   target.action_values().outputs() =
       SubstitutionList::MakeForTest("//out/Debug/{{source_name_part}}.out");
 
-  setup.build_settings()->set_python_path(
+  setup.build_settings()->SetPythonPath(
       base::FilePath(FILE_PATH_LITERAL("/usr/bin/python")));
 
   std::ostringstream out;
@@ -478,7 +478,7 @@
   Err err;
   TestWithScope setup;
 
-  setup.build_settings()->set_python_path(
+  setup.build_settings()->SetPythonPath(
       base::FilePath(FILE_PATH_LITERAL("/usr/bin/python")));
 
   Target dep(setup.settings(), Label(SourceDir("//foo/"), "dep"));
@@ -552,7 +552,7 @@
   Err err;
   TestWithScope setup;
 
-  setup.build_settings()->set_python_path(
+  setup.build_settings()->SetPythonPath(
       base::FilePath(FILE_PATH_LITERAL("/usr/bin/python")));
 
   Config farcfg(setup.settings(), Label(SourceDir("//foo/"), "farcfg"));
@@ -626,7 +626,7 @@
   target.SetToolchain(setup.toolchain());
   ASSERT_TRUE(target.OnResolved(&err));
 
-  setup.build_settings()->set_python_path(
+  setup.build_settings()->SetPythonPath(
       base::FilePath(FILE_PATH_LITERAL("/Program Files/python")));
 
   std::ostringstream out;
diff --git a/src/gn/setup.cc b/src/gn/setup.cc
index 49830ae..b29e2ff 100644
--- a/src/gn/setup.cc
+++ b/src/gn/setup.cc
@@ -829,7 +829,7 @@
   if (cmdline.HasSwitch(switches::kScriptExecutable)) {
     auto script_executable =
         cmdline.GetSwitchValuePath(switches::kScriptExecutable);
-    build_settings_.set_python_path(ProcessFileExtensions(script_executable));
+    build_settings_.SetPythonPath(ProcessFileExtensions(script_executable));
   } else if (value) {
     if (!value->VerifyTypeIs(Value::STRING, err)) {
       return false;
@@ -846,7 +846,7 @@
         return false;
       }
     }
-    build_settings_.set_python_path(python_path);
+    build_settings_.SetPythonPath(std::move(python_path));
   } else {
 #if defined(OS_WIN)
     base::FilePath python_path =
@@ -857,9 +857,9 @@
                      "just \"python.exe\"");
       python_path = base::FilePath(u"python.exe");
     }
-    build_settings_.set_python_path(python_path);
+    build_settings_.SetPythonPath(std::move(python_path));
 #else
-    build_settings_.set_python_path(base::FilePath("python"));
+    build_settings_.SetPythonPath(base::FilePath("python"));
 #endif
   }
   return true;
diff --git a/src/gn/setup_unittest.cc b/src/gn/setup_unittest.cc
index d9ace51..547c282 100644
--- a/src/gn/setup_unittest.cc
+++ b/src/gn/setup_unittest.cc
@@ -410,3 +410,145 @@
   EXPECT_TRUE(dependency_includes_file("build_defines.gni"));
   EXPECT_TRUE(dependency_includes_file("params.gni"));
 }
+
+TEST_F(SetupTest, AbsolutePythonPathInsideRootDir) {
+  base::CommandLine cmdline(base::CommandLine::NO_PROGRAM);
+
+  const char kDotfileContents[] = R"(
+buildconfig = "//BUILDCONFIG.gn"
+script_executable = ""
+)";
+
+  // Create a temp directory containing a .gn file and a BUILDCONFIG.gn file,
+  // pass it as --root.
+  base::ScopedTempDir in_temp_dir;
+  ASSERT_TRUE(in_temp_dir.CreateUniqueTempDir());
+  base::FilePath in_path = in_temp_dir.GetPath();
+  base::FilePath dot_gn_name = in_path.Append(FILE_PATH_LITERAL(".gn"));
+  WriteFile(dot_gn_name, kDotfileContents);
+
+  base::FilePath absolute_bin_dir = in_path.Append(FILE_PATH_LITERAL("bin"));
+  base::FilePath script_executable =
+      absolute_bin_dir.Append(FILE_PATH_LITERAL("python"));
+
+  WriteFile(in_path.Append(FILE_PATH_LITERAL("BUILDCONFIG.gn")), "");
+  cmdline.AppendSwitchPath(switches::kRoot, in_path);
+  cmdline.AppendSwitchPath(switches::kScriptExecutable, script_executable);
+
+  base::FilePath build_dir = in_path.Append(FILE_PATH_LITERAL("out"));
+
+  // Run setup and check that python_path_is_relative_to_build_dir is true and
+  // python_path is relative to the build directory.
+  Setup setup;
+  Err err;
+  EXPECT_TRUE(
+      setup.DoSetupWithErr(FilePathToUTF8(build_dir), true, cmdline, &err));
+  EXPECT_TRUE(setup.build_settings().python_path_is_relative_to_build_dir());
+  EXPECT_EQ(setup.build_settings().python_path(),
+            base::FilePath(FILE_PATH_LITERAL("../bin/python")));
+}
+
+TEST_F(SetupTest, AbsolutePythonPathOutsideRootDir) {
+  base::CommandLine cmdline(base::CommandLine::NO_PROGRAM);
+
+  const char kDotfileContents[] = R"(
+buildconfig = "//BUILDCONFIG.gn"
+script_executable = ""
+)";
+
+  // Create a temp directory containing a .gn file and a BUILDCONFIG.gn file,
+  // pass it as --root.
+  base::ScopedTempDir in_temp_dir;
+  ASSERT_TRUE(in_temp_dir.CreateUniqueTempDir());
+  base::FilePath in_path = in_temp_dir.GetPath();
+  base::FilePath dot_gn_name = in_path.Append(FILE_PATH_LITERAL(".gn"));
+  WriteFile(dot_gn_name, kDotfileContents);
+
+  base::ScopedTempDir other_temp_dir;
+  ASSERT_TRUE(other_temp_dir.CreateUniqueTempDir());
+  base::FilePath absolute_bin_dir =
+      other_temp_dir.GetPath().Append(FILE_PATH_LITERAL("bin"));
+  base::FilePath script_executable =
+      absolute_bin_dir.Append(FILE_PATH_LITERAL("python"));
+
+  WriteFile(in_path.Append(FILE_PATH_LITERAL("BUILDCONFIG.gn")), "");
+  cmdline.AppendSwitchPath(switches::kRoot, in_path);
+  cmdline.AppendSwitchPath(switches::kScriptExecutable, script_executable);
+
+  base::FilePath build_dir = in_path.Append(FILE_PATH_LITERAL("out"));
+
+  // Run setup and check that python_path_is_relative_to_build_dir is false and
+  // python_path is unchanged (apart from normalization).
+  Setup setup;
+  Err err;
+  EXPECT_TRUE(
+      setup.DoSetupWithErr(FilePathToUTF8(build_dir), true, cmdline, &err));
+  EXPECT_FALSE(setup.build_settings().python_path_is_relative_to_build_dir());
+  EXPECT_EQ(setup.build_settings().python_path(),
+            script_executable.NormalizePathSeparatorsTo('/'));
+}
+
+TEST_F(SetupTest, RelativePythonPath) {
+  base::CommandLine cmdline(base::CommandLine::NO_PROGRAM);
+
+  const char kDotfileContents[] = R"(
+buildconfig = "//BUILDCONFIG.gn"
+script_executable = ""
+)";
+
+  // Create a temp directory containing a .gn file and a BUILDCONFIG.gn file,
+  // pass it as --root.
+  base::ScopedTempDir in_temp_dir;
+  ASSERT_TRUE(in_temp_dir.CreateUniqueTempDir());
+  base::FilePath in_path = in_temp_dir.GetPath();
+  base::FilePath dot_gn_name = in_path.Append(FILE_PATH_LITERAL(".gn"));
+  WriteFile(dot_gn_name, kDotfileContents);
+
+  base::FilePath relative_bin_dir(FILE_PATH_LITERAL("bin"));
+  base::FilePath script_executable =
+      relative_bin_dir.Append(FILE_PATH_LITERAL("python"));
+
+#if defined(OS_WIN)
+  // On Windows, if script executable is a relative path, then it must exist in
+  // either the current directory or PATH with a `.exe` or `.bat` extension,
+  // otherwise `FindWindowsPython` fails.
+  base::FilePath original_cwd;
+  base::GetCurrentDirectory(&original_cwd);
+
+  // Switch to another temporary directory for the test.
+  base::ScopedTempDir cwd_temp_dir;
+  ASSERT_TRUE(cwd_temp_dir.CreateUniqueTempDir());
+
+  base::FilePath absolute_script_executable = cwd_temp_dir.GetPath()
+                                                  .Append(script_executable)
+                                                  .ReplaceExtension(u".exe");
+  ASSERT_TRUE(base::CreateDirectoryAndGetError(
+      absolute_script_executable.DirName(), nullptr));
+  WriteFile(absolute_script_executable, "");
+  base::SetCurrentDirectory(cwd_temp_dir.GetPath());
+#endif
+
+  WriteFile(in_path.Append(FILE_PATH_LITERAL("BUILDCONFIG.gn")), "");
+  cmdline.AppendSwitchPath(switches::kRoot, in_path);
+  cmdline.AppendSwitchPath(switches::kScriptExecutable, script_executable);
+
+  base::FilePath build_dir = in_path.Append(FILE_PATH_LITERAL("out"));
+
+  // Run setup and check that python_path_is_relative_to_build_dir is false and
+  // python_path is made absolute on Windows, and unchanged on other platforms.
+  Setup setup;
+  Err err;
+  EXPECT_TRUE(
+      setup.DoSetupWithErr(FilePathToUTF8(build_dir), true, cmdline, &err));
+  EXPECT_FALSE(setup.build_settings().python_path_is_relative_to_build_dir());
+
+#if defined(OS_WIN)
+  EXPECT_EQ(setup.build_settings().python_path(),
+            absolute_script_executable.NormalizePathSeparatorsTo('/'));
+
+  // Change back to the original cwd.
+  base::SetCurrentDirectory(original_cwd);
+#else
+  EXPECT_EQ(setup.build_settings().python_path(), script_executable);
+#endif
+}