diff --git a/test/test_other.py b/test/test_other.py
index 2642b9aafd82c..1ae34b5c98081 100644
--- a/test/test_other.py
+++ b/test/test_other.py
@@ -10409,7 +10409,7 @@ def test_dwarf_system_lib(self):
         [LLVM_DWARFDUMP, libc, '-debug-info', '-debug-line', '--recurse-depth=0'],
         stdout=PIPE).stdout
     # Check that the embedded location of the source file is correct.
-    self.assertIn('DW_AT_name\t("system/lib/emmalloc.c")', dwdump)
+    self.assertIn('DW_AT_name\t("/emsdk/emscripten/system/lib/emmalloc.c")', dwdump)
     self.assertIn('DW_AT_comp_dir\t("/emsdk/emscripten")', dwdump)
 
   @parameterized({
diff --git a/tools/system_libs.py b/tools/system_libs.py
index e6bbf1c3435b1..3b01a85fbf651 100644
--- a/tools/system_libs.py
+++ b/tools/system_libs.py
@@ -42,6 +42,10 @@
 # link time.
 USE_NINJA = int(os.environ.get('EMCC_USE_NINJA', '0'))
 
+# A (fake) deterministic emscripten path to use in __FILE__ macro and debug info
+# to produce reproducible builds across platforms.
+DETERMINISITIC_PREFIX = '/emsdk/emscripten'
+
 
 def files_in_path(path, filenames):
   srcdir = utils.path_from_root(path)
@@ -472,9 +476,9 @@ def generate_ninja(self, build_dir, libname):
     if self.deterministic_paths:
       source_dir = utils.path_from_root()
       relative_source_dir = os.path.relpath(source_dir, build_dir)
-      cflags += [f'-ffile-prefix-map={source_dir}=/emsdk/emscripten',
-                 f'-ffile-prefix-map={relative_source_dir}/=',
-                 '-fdebug-compilation-dir=/emsdk/emscripten']
+      cflags += [f'-ffile-prefix-map={source_dir}={DETERMINISITIC_PREFIX}',
+                 f'-ffile-prefix-map={relative_source_dir}={DETERMINISITIC_PREFIX}',
+                 f'-fdebug-compilation-dir={DETERMINISITIC_PREFIX}']
     asflags = get_base_cflags(preprocess=False)
     input_files = self.get_files()
     ninja_file = os.path.join(build_dir, 'build.ninja')
@@ -496,9 +500,9 @@ def build_objects(self, build_dir):
       source_dir = utils.path_from_root()
       if batch_inputs:
         relative_source_dir = os.path.relpath(source_dir, build_dir)
-        cflags += [f'-ffile-prefix-map={relative_source_dir}/=']
-      cflags += [f'-ffile-prefix-map={source_dir}=/emsdk/emscripten',
-                 '-fdebug-compilation-dir=/emsdk/emscripten']
+        cflags += [f'-ffile-prefix-map={relative_source_dir}={DETERMINISITIC_PREFIX}']
+      cflags += [f'-ffile-prefix-map={source_dir}={DETERMINISITIC_PREFIX}',
+                 f'-fdebug-compilation-dir={DETERMINISITIC_PREFIX}']
     case_insensitive = is_case_insensitive(build_dir)
     for src in self.get_files():
       ext = shared.suffix(src)