diff --git a/build/toolchain/win/BUILD.gn b/build/toolchain/win/BUILD.gn
index bc54953b58e..5bce92ec533 100644
--- a/build/toolchain/win/BUILD.gn
+++ b/build/toolchain/win/BUILD.gn
@@ -22,6 +22,8 @@ assert(is_win)
 # This tool will is used as a wrapper for various commands below.
 tool_wrapper_path = rebase_path("tool_wrapper.py", root_build_dir)
 
+ninja_path = rebase_path("//buildtools/ninja/ninja")
+
 if (use_goma) {
   goma_prefix = "$goma_dir/gomacc.exe "
 } else {
@@ -72,7 +74,7 @@ template("msvc_toolchain") {
       # TODO(brettw) enable this when GN support in the binary has been rolled.
       #precompiled_header_type = "msvc"
       pdbname = "{{target_out_dir}}/{{target_output_name}}_c.pdb"
-      command = "ninja -t msvc -e $env -- $cl /nologo /showIncludes /FC @$rspfile /c {{source}} /Fo{{output}} /Fd$pdbname"
+      command = "$ninja_path -t msvc -e $env -- $cl /nologo /showIncludes /FC @$rspfile /c {{source}} /Fo{{output}} /Fd$pdbname"
       depsformat = "msvc"
       description = "CC {{output}}"
       outputs = [
@@ -93,7 +95,7 @@ template("msvc_toolchain") {
       if (is_clang && invoker.current_cpu == "x86") {
         flags = "-m32"
       }
-      command = "ninja -t msvc -e $env -- $cl $flags /nologo /showIncludes /FC @$rspfile /c {{source}} /Fo{{output}} /Fd$pdbname"
+      command = "$ninja_path -t msvc -e $env -- $cl $flags /nologo /showIncludes /FC @$rspfile /c {{source}} /Fo{{output}} /Fd$pdbname"
       depsformat = "msvc"
       description = "CXX {{output}}"
       outputs = [
diff --git a/runtime/third_party/binary_size/src/explain_binary_size_delta.py b/runtime/third_party/binary_size/src/explain_binary_size_delta.py
index 13f7c120237..ecf59a431f2 100755
--- a/runtime/third_party/binary_size/src/explain_binary_size_delta.py
+++ b/runtime/third_party/binary_size/src/explain_binary_size_delta.py
@@ -15,7 +15,7 @@ dumps. Example:
 
   # obtain symbol data from first binary in /tmp/nm1.dump
   cd $CHECKOUT1_SRC
-  ninja -C out/Release binary_size_tool
+  buildtools/ninja/ninja -C out/Release binary_size_tool
   tools/binary_size/run_binary_size_analysis \
       --library <path_to_library>
       --destdir /tmp/throwaway
@@ -23,7 +23,7 @@ dumps. Example:
 
   # obtain symbol data from second binary in /tmp/nm2.dump
   cd $CHECKOUT2_SRC
-  ninja -C out/Release binary_size_tool
+  buildtools/ninja/ninja -C out/Release binary_size_tool
   tools/binary_size/run_binary_size_analysis \
       --library <path_to_library>
       --destdir /tmp/throwaway
diff --git a/runtime/tools/wiki/xref_extractor/bin/main.dart b/runtime/tools/wiki/xref_extractor/bin/main.dart
index f24a9fd7c3b..b785dc71171 100644
--- a/runtime/tools/wiki/xref_extractor/bin/main.dart
+++ b/runtime/tools/wiki/xref_extractor/bin/main.dart
@@ -88,7 +88,7 @@ Usage: dart runtime/tools/wiki/xref_extractor/bin/main.dart <path-to-cquery>
 /// same input C++ files and this greatly confuses cquery.
 Future<void> generateCompileCommands() async {
   print('Extracting compilation commands from build files for ReleaseX64');
-  final result = await Process.run('ninja', [
+  final result = await Process.run('buildtools/ninja/ninja', [
     '-C',
     '${Platform.isMacOS ? 'xcodebuild' : 'out'}/ReleaseX64',
     '-t',
diff --git a/tools/build.py b/tools/build.py
index aa0f6253ffc..296fe618aee 100755
--- a/tools/build.py
+++ b/tools/build.py
@@ -167,7 +167,7 @@ def BuildOneConfig(options, targets, target_os, mode, arch, sanitizer):
     build_config = utils.GetBuildConf(mode, arch, target_os, sanitizer)
     out_dir = utils.GetBuildRoot(HOST_OS, mode, arch, target_os, sanitizer)
     using_goma = False
-    command = ['ninja', '-C', out_dir]
+    command = ['buildtools/ninja/ninja', '-C', out_dir]
     if options.verbose:
         command += ['-v']
     if UseGoma(out_dir):
diff --git a/tools/generate_idefiles.py b/tools/generate_idefiles.py
index afe4d5793e6..6b68ef44aa7 100755
--- a/tools/generate_idefiles.py
+++ b/tools/generate_idefiles.py
@@ -12,6 +12,7 @@ analysis_options.yaml for the Dart analyzer.
 import argparse
 import json
 import os
+import re
 import subprocess
 import sys
 
@@ -76,7 +77,8 @@ def GenerateCompileCommands(options):
         # Remove ninja prepend on Windows.
         # This is not fully correct, as now it fails to find a sysroot for
         # Windows. However, clangd completely fails with the `-t` flag.
-        command = command.replace("ninja -t msvc -e environment.x64 --", "")
+        command = re.sub(r"([^\s]*)ninja -t msvc -e environment.x64 --", "",
+                         command)
 
         # Add sysroot from out\DebugX64\environment.x64 on Windows.
         # TODO(dacoharkes): Fetch the paths from that file.
diff --git a/tools/linux_dist_support/run_debian_build.sh b/tools/linux_dist_support/run_debian_build.sh
index 4f096636583..b36eefedb7b 100755
--- a/tools/linux_dist_support/run_debian_build.sh
+++ b/tools/linux_dist_support/run_debian_build.sh
@@ -4,8 +4,8 @@
 # BSD-style license that can be found in the LICENSE file.
 set -x
 
-ninja=$(which ninja)
-depot_tools=$(dirname $ninja)
+fetch=$(which fetch)
+depot_tools=$(dirname $fetch)
 image="debian-package:0.1"
 dockerfile=tools/linux_dist_support/Debian.dockerfile
 docker build --build-arg depot_tools=$depot_tools -t $image - < $dockerfile