diff --git a/scripts/clang-tools/gen_compile_commands.py b/scripts/clang-tools/gen_compile_commands.py
index 180952fb91c1..5dea4479240b 100755
--- a/scripts/clang-tools/gen_compile_commands.py
+++ b/scripts/clang-tools/gen_compile_commands.py
@@ -64,7 +64,7 @@ def parse_arguments():
     args = parser.parse_args()
 
     return (args.log_level,
-            os.path.abspath(args.directory),
+            os.path.realpath(args.directory),
             args.output,
             args.ar,
             args.paths if len(args.paths) > 0 else [args.directory])
@@ -172,8 +172,8 @@ def process_line(root_directory, command_prefix, file_path):
     # by Make, so this code replaces the escaped version with '#'.
     prefix = command_prefix.replace('\#', '#').replace('$(pound)', '#')
 
-    # Use os.path.abspath() to normalize the path resolving '.' and '..' .
-    abs_path = os.path.abspath(os.path.join(root_directory, file_path))
+    # Return the canonical path, eliminating any symbolic links encountered in the path.
+    abs_path = os.path.realpath(os.path.join(root_directory, file_path))
     if not os.path.exists(abs_path):
         raise ValueError('File %s not found' % abs_path)
     return {