diff --git a/src/flake8/plugins/pyflakes.py b/src/flake8/plugins/pyflakes.py
index a9dbc4c..f165c95 100644
--- a/src/flake8/plugins/pyflakes.py
+++ b/src/flake8/plugins/pyflakes.py
@@ -3,6 +3,7 @@ from __future__ import annotations
 
 import argparse
 import ast
+import logging
 import os
 from typing import Any
 from typing import Generator
@@ -12,6 +13,8 @@ import pyflakes.checker
 from flake8 import utils
 from flake8.options.manager import OptionManager
 
+LOG = logging.getLogger(__name__)
+
 FLAKE8_PYFLAKES_CODES = {
     "UnusedImport": "F401",
     "ImportShadowedByLoopVar": "F402",
@@ -137,6 +140,12 @@ class FlakesChecker(pyflakes.checker.Checker):
             cls.builtIns = cls.builtIns.union(options.builtins)
         cls.with_doctest = options.doctests
 
+        if options.include_in_doctest or options.exclude_from_doctest:
+            LOG.warning(
+                "--include-in-doctest / --exclude-from-doctest will be "
+                "removed in a future version.  see PyCQA/flake8#1747"
+            )
+
         included_files = []
         for included_file in options.include_in_doctest:
             if included_file == "":