diff --git a/Lib/test/test_build_details.py b/Lib/test/test_build_details.py
index b6f4b6fe26379b..7ee73614462e51 100644
--- a/Lib/test/test_build_details.py
+++ b/Lib/test/test_build_details.py
@@ -217,6 +217,24 @@ def test_round_trip(self):
         self.assertEqual(data_abs_path['base_prefix'],
                          data_rel_path['base_prefix'])
 
+        self.check_relative_paths(data_abs_path, data_rel_path)
+
+    def test_round_trip_with_config_file_path(self):
+        data_abs_path = self.build_details_absolute_paths
+        base_prefix = data_abs_path['base_prefix']
+        config_dir = os.path.join(base_prefix, 'lib', 'python3.X')
+        data_rel_path = self.build_details_absolute_paths
+        generate_build_details.make_paths_relative(
+            data_rel_path,
+            config_path=os.path.join(config_dir, 'build-details.json'),
+        )
+
+        # base_prefix is relative to the config file's directory...
+        self.assertEqual(data_rel_path['base_prefix'], os.path.join('..', '..'))
+        # ...while the other paths are still relative to base_prefix.
+        self.check_relative_paths(data_abs_path, data_rel_path)
+
+    def check_relative_paths(self, data_abs_path, data_rel_path):
         base_prefix = data_abs_path['base_prefix']
 
         top_level_keys = ('base_interpreter',)
diff --git a/Misc/NEWS.d/next/Build/2026-10-20-23-30-00.gh-issue-160004.CfgPth.rst b/Misc/NEWS.d/next/Build/2026-10-20-23-30-00.gh-issue-160004.CfgPth.rst
new file mode 100644
index 00000000000000..57de41ae87aaae
--- /dev/null
+++ b/Misc/NEWS.d/next/Build/2026-10-20-23-30-00.gh-issue-160004.CfgPth.rst
@@ -0,0 +1,4 @@
+Fix the paths in the :pep:`739` ``build-details.json`` file generated by
+:file:`Tools/build/generate-build-details.py` with both ``--relative-paths``
+and ``--config-file-path``. They are now relative to ``base_prefix``, as
+required, instead of being computed from the already relative ``base_prefix``.
diff --git a/Tools/build/generate-build-details.py b/Tools/build/generate-build-details.py
index 738c51026b77cc..d3ccc9f5f76c84 100644
--- a/Tools/build/generate-build-details.py
+++ b/Tools/build/generate-build-details.py
@@ -142,11 +142,12 @@ def generate_data(schema_version: str) -> collections.defaultdict[str, Any]:
 
 
 def make_paths_relative(data: dict[str, Any], config_path: str | None = None) -> None:
-    # Make base_prefix relative to the config_path directory
+    base_prefix = data['base_prefix']
+    # Make base_prefix relative to the config_path directory.  The other paths
+    # are still made relative to the absolute base_prefix below.
     if config_path:
-        data['base_prefix'] = relative_path(data['base_prefix'],
+        data['base_prefix'] = relative_path(base_prefix,
                                             os.path.dirname(config_path))
-    base_prefix = data['base_prefix']
 
     # Update path values to make them relative to base_prefix
     PATH_KEYS = (