diff --git a/modules/python/src2/copy_typings_stubs_on_success.py b/modules/python/src2/copy_typings_stubs_on_success.py
index efcf84ee82..eb5a2e4e6c 100644
--- a/modules/python/src2/copy_typings_stubs_on_success.py
+++ b/modules/python/src2/copy_typings_stubs_on_success.py
@@ -13,6 +13,21 @@ else:
     from distutils.dir_util import copy_tree
 
 
+def _remove_stale_pyi_files(directory):
+    """Remove .pyi files and py.typed markers from the directory tree.
+
+    During incremental builds, disabling a previously enabled module leaves
+    stale typing stubs in the loader directory from a previous copy.  Since
+    copy_tree merges rather than replaces, those stale files persist.
+    Removing all stub files before copying ensures only stubs for currently
+    enabled modules are present.  Runtime .py files are not affected.
+    """
+    for dirpath, dirnames, filenames in os.walk(directory):
+        for fname in filenames:
+            if fname.endswith('.pyi') or fname == 'py.typed':
+                os.remove(os.path.join(dirpath, fname))
+
+
 def main():
     args = parse_arguments()
     py_typed_path = os.path.join(args.stubs_dir, 'py.typed')
@@ -24,6 +39,8 @@ def main():
             'generation phase.'.format(py_typed_path)
         )
         return
+    if os.path.isdir(args.output_dir):
+        _remove_stale_pyi_files(args.output_dir)
     copy_tree(args.stubs_dir, args.output_dir)
 
 
diff --git a/modules/python/src2/typing_stubs_generation/generation.py b/modules/python/src2/typing_stubs_generation/generation.py
index 07de26c0af..f27f64df0a 100644
--- a/modules/python/src2/typing_stubs_generation/generation.py
+++ b/modules/python/src2/typing_stubs_generation/generation.py
@@ -3,6 +3,7 @@ __all__ = ("generate_typing_stubs", )
 from io import StringIO
 from pathlib import Path
 import re
+import shutil
 from typing import (Callable, NamedTuple, Union, Set, Dict,
                     Collection, Tuple, List)
 import warnings
@@ -24,6 +25,22 @@ from .nodes.type_node import (TypeNode, AliasTypeNode, AliasRefTypeNode,
                               ConditionalAliasTypeNode, PrimitiveTypeNode)
 
 
+def _clean_stale_stubs_dirs(stubs_root: Path) -> None:
+    """Remove all subdirectories under stubs_root.
+
+    During incremental builds, disabling a previously enabled module leaves
+    behind its typing stub directory (e.g. cv2/gapi/).  Removing all
+    subdirectories before regeneration ensures only stubs for currently
+    enabled modules are present.  Top-level files (py.typed, __init__.pyi)
+    are kept because they are managed separately.
+    """
+    if not stubs_root.is_dir():
+        return
+    for item in stubs_root.iterdir():
+        if item.is_dir():
+            shutil.rmtree(item)
+
+
 def generate_typing_stubs(root: NamespaceNode, output_path: Path):
     """Generates typing stubs for the AST with root `root` and outputs
     created files tree to directory pointed by `output_path`.
@@ -88,6 +105,12 @@ def generate_typing_stubs(root: NamespaceNode, output_path: Path):
     # The whole process should fail !only! when all possible scopes are
     # checked and at least 1 node is still unresolved.
     root.resolve_type_nodes()
+    # Remove stale typing stub subdirectories from previous builds.
+    # In incremental builds, disabling a module (e.g. -DBUILD_opencv_gapi=OFF)
+    # no longer generates its stubs, but leftover directories from a previous
+    # build persist and propagate through the copy/install steps, causing
+    # type-checker errors for stubs referencing unavailable modules.
+    _clean_stale_stubs_dirs(Path(output_path) / root.export_name)
     _generate_typing_module(root, output_path)
     _populate_reexported_symbols(root)
     _generate_typing_stubs(root, output_path)