diff --git a/kokoro/windows/x64/build.bat b/kokoro/windows/x64/build.bat
index 2bed6a1ad7..6ed3a2e226 100644
--- a/kokoro/windows/x64/build.bat
+++ b/kokoro/windows/x64/build.bat
@@ -3,27 +3,25 @@ set OUTPUT_DIRECTORY=Release_x64
 set GYP_DEFINES=target_arch=x64
 
 set ROOTDIR=%cd%
-set PACKAGERDIR=%ROOTDIR%\git\packager
-
-:: TODO(rkuroiwa): There are several `dir`s in this script to figure out the
-:: directory structure created by the builder. Remove them.
-dir
-
-dir ..
+set PACKAGERDIR=%ROOTDIR%\git\src
 
 :: TODO(rkuroiwa): Put this in a batch script and source it, so that this
 :: doesn't need to be copied for all configurations.
-git clone https://chromium.googlesource.com/chromium/tools/depot_tools.git ..\depot_tools\
-set DEPOTTOOLSDIR=%ROOTDIR%\..\depot_tools
+git clone "https://chromium.googlesource.com/chromium/tools/depot_tools.git" depot_tools
+set DEPOTTOOLSDIR=%ROOTDIR%\depot_tools
 
-python %PACKAGERDIR%\kokoro\deps_replacer.py "github.com" "github.googlesource.com"
+python %PACKAGERDIR%\kokoro\deps_replacer.py "https://github.com" "https://github.googlesource.com"
 
 cd %PACKAGERDIR%\..
-dir
-move packager src
 
-%DEPOTTOOLSDIR%\gclient config https://github.com/google/shaka-packager.git --name=src --unmanaged
-%DEPOTTOOLSDIR%\gclient sync
+:: Note that gclient file is a batch script, so 'call' must be used to wait for
+:: the result.
+:: Also gclient turns off echo, so echo is re-enabled after the command.
+call %DEPOTTOOLSDIR%\gclient config "https://github.com/google/shaka-packager.git" --name=src --unmanaged
+echo on
+call %DEPOTTOOLSDIR%\gclient sync
+echo on
+
 cd src
 %DEPOTTOOLSDIR%\ninja -C "out\%OUTPUT_DIRECTORY%" -k 100
 
diff --git a/kokoro/windows/x64/continuous.cfg b/kokoro/windows/x64/continuous.cfg
index 4ac46a645d..36b8c2beb6 100644
--- a/kokoro/windows/x64/continuous.cfg
+++ b/kokoro/windows/x64/continuous.cfg
@@ -1 +1 @@
-build_file: "packager/kokoro/windows/x64/build.bat"
+build_file: "src/kokoro/windows/x64/build.bat"
diff --git a/kokoro/windows/x64/presubmit.cfg b/kokoro/windows/x64/presubmit.cfg
index 4ac46a645d..36b8c2beb6 100644
--- a/kokoro/windows/x64/presubmit.cfg
+++ b/kokoro/windows/x64/presubmit.cfg
@@ -1 +1 @@
-build_file: "packager/kokoro/windows/x64/build.bat"
+build_file: "src/kokoro/windows/x64/build.bat"