diff --git a/scripts/gen_compile_commands.py b/scripts/gen_compile_commands.py
index 535248cf2d7e..49fff0b0b385 100755
--- a/scripts/gen_compile_commands.py
+++ b/scripts/gen_compile_commands.py
@@ -59,23 +59,21 @@ def parse_arguments():
     return args.log_level, directory, output
 
 
-def process_line(root_directory, file_directory, command_prefix, relative_path):
+def process_line(root_directory, command_prefix, file_path):
     """Extracts information from a .cmd line and creates an entry from it.
 
     Args:
         root_directory: The directory that was searched for .cmd files. Usually
             used directly in the "directory" entry in compile_commands.json.
-        file_directory: The path to the directory the .cmd file was found in.
         command_prefix: The extracted command line, up to the last element.
-        relative_path: The .c file from the end of the extracted command.
-            Usually relative to root_directory, but sometimes relative to
-            file_directory and sometimes neither.
+        file_path: The .c file from the end of the extracted command.
+            Usually relative to root_directory, but sometimes absolute.
 
     Returns:
         An entry to append to compile_commands.
 
     Raises:
-        ValueError: Could not find the extracted file based on relative_path and
+        ValueError: Could not find the extracted file based on file_path and
             root_directory or file_directory.
     """
     # The .cmd files are intended to be included directly by Make, so they
@@ -84,20 +82,14 @@ def process_line(root_directory, file_directory, command_prefix, relative_path):
     # by Make, so this code replaces the escaped version with '#'.
     prefix = command_prefix.replace('\#', '#').replace('$(pound)', '#')
 
-    cur_dir = root_directory
-    expected_path = os.path.join(cur_dir, relative_path)
-    if not os.path.exists(expected_path):
-        # Try using file_directory instead. Some of the tools have a different
-        # style of .cmd file than the kernel.
-        cur_dir = file_directory
-        expected_path = os.path.join(cur_dir, relative_path)
-        if not os.path.exists(expected_path):
-            raise ValueError('File %s not in %s or %s' %
-                             (relative_path, root_directory, file_directory))
+    # Use os.path.abspath() to normalize the path resolving '.' and '..' .
+    abs_path = os.path.abspath(os.path.join(root_directory, file_path))
+    if not os.path.exists(abs_path):
+        raise ValueError('File %s not found' % abs_path)
     return {
-        'directory': cur_dir,
-        'file': relative_path,
-        'command': prefix + relative_path,
+        'directory': root_directory,
+        'file': abs_path,
+        'command': prefix + file_path,
     }
 
 
@@ -122,7 +114,7 @@ def main():
                 result = line_matcher.match(f.readline())
                 if result:
                     try:
-                        entry = process_line(directory, dirpath,
+                        entry = process_line(directory,
                                              result.group(1), result.group(2))
                         compile_commands.append(entry)
                     except ValueError as err: