diff --git a/tools/gn/bootstrap/bootstrap.py b/tools/gn/bootstrap/bootstrap.py
index 61146e0..35c0945 100755
--- a/tools/gn/bootstrap/bootstrap.py
+++ b/tools/gn/bootstrap/bootstrap.py
@@ -936,6 +936,13 @@
   cmd.append('gn')
   check_call(cmd)
 
+  # build.ninja currently refers back to gn from the temporary directory.
+  # Regenerate the build files using the gn we just built so that the reference
+  # gets updated to "./gn".
+  cmd = [os.path.join(build_dir, 'gn'), 'gen', build_dir,
+         '--args=%s' % gn_gen_args]
+  check_call(cmd)
+
   if not options.debug and not is_win:
     check_call(['strip', os.path.join(build_dir, 'gn')])
 
diff --git a/tools/gn/filesystem_utils.cc b/tools/gn/filesystem_utils.cc
index b1370e8..6cce895 100644
--- a/tools/gn/filesystem_utils.cc
+++ b/tools/gn/filesystem_utils.cc
@@ -441,10 +441,20 @@
     relative_components.push_back(base::FilePath::kParentDirectory);
   for (size_t j = i; j < target_components.size(); j++)
     relative_components.push_back(target_components[j]);
-  base::FilePath relative(base::FilePath::kCurrentDirectory);
-  for (const auto& component : relative_components)
-    relative = relative.Append(component);
-  return relative;
+  if (relative_components.size() <= 1) {
+    // In case the file pointed-to is an executable, prepend the current
+    // directory to the path -- if the path was "gn", use "./gn" instead.  If
+    // the file path is used in a command, this prevents issues where "gn" might
+    // not be in the PATH (or it is in the path, and the wrong gn is used).
+    relative_components.insert(relative_components.begin(),
+                               base::FilePath::kCurrentDirectory);
+  }
+  // base::FilePath::Append(component) replaces the file path with |component|
+  // if the path is base::Filepath::kCurrentDirectory.  We want to preserve the
+  // leading "./", so we build the path ourselves and use that to construct the
+  // base::FilePath.
+  base::FilePath::StringType separator(&base::FilePath::kSeparators[0], 1);
+  return base::FilePath(base::JoinString(relative_components, separator));
 }
 
 void NormalizePath(std::string* path, const base::StringPiece& source_root) {
diff --git a/tools/gn/filesystem_utils_unittest.cc b/tools/gn/filesystem_utils_unittest.cc
index 03ec780..dc2e512 100644
--- a/tools/gn/filesystem_utils_unittest.cc
+++ b/tools/gn/filesystem_utils_unittest.cc
@@ -179,6 +179,10 @@
       base::FilePath(L"out\\Debug"),
       MakeAbsoluteFilePathRelativeIfPossible(
           base::FilePath(L"C:\\src"), base::FilePath(L"C:\\src\\out\\Debug")));
+  EXPECT_EQ(base::FilePath(L".\\gn"),
+            MakeAbsoluteFilePathRelativeIfPossible(
+                base::FilePath(L"C:\\src\\out\\Debug"),
+                base::FilePath(L"C:\\src\\out\\Debug\\gn")));
   EXPECT_EQ(
       base::FilePath(L"..\\.."),
       MakeAbsoluteFilePathRelativeIfPossible(
@@ -197,6 +201,9 @@
   EXPECT_EQ(base::FilePath("out/Debug"),
             MakeAbsoluteFilePathRelativeIfPossible(
                 base::FilePath("/src"), base::FilePath("/src/out/Debug")));
+  EXPECT_EQ(base::FilePath("./gn"), MakeAbsoluteFilePathRelativeIfPossible(
+                                        base::FilePath("/src/out/Debug"),
+                                        base::FilePath("/src/out/Debug/gn")));
   EXPECT_EQ(base::FilePath("../.."),
             MakeAbsoluteFilePathRelativeIfPossible(
                 base::FilePath("/src/out/Debug"), base::FilePath("/src")));