diff --git a/doc/whats_new/v0.20.rst b/doc/whats_new/v0.20.rst
index d148d0b40c74f..f0e570ac70413 100644
--- a/doc/whats_new/v0.20.rst
+++ b/doc/whats_new/v0.20.rst
@@ -85,6 +85,14 @@ Changelog
   where ``max_features`` was sometimes rounded down to zero.
   :issue:`12388` by :user:`Connor Tann <Connossor>`.
 
+:mod:`sklearn.feature_extraction`
+...........................
+
+- |Fix| Fixed a regression in v0.20.0 where
+  :func:`feature_extraction.text.CountVectorizer` and other text vectorizers
+  could error during stop words validation with custom preprocessors
+  or tokenizers. :issue:`12393` by `Roman Yurchak`_.
+
 :mod:`sklearn.linear_model`
 ...........................
 
diff --git a/sklearn/feature_extraction/tests/test_text.py b/sklearn/feature_extraction/tests/test_text.py
index 503c62b2b3de3..9798175e4d5bc 100644
--- a/sklearn/feature_extraction/tests/test_text.py
+++ b/sklearn/feature_extraction/tests/test_text.py
@@ -1,4 +1,5 @@
 from __future__ import unicode_literals
+import re
 import warnings
 
 import pytest
@@ -1121,6 +1122,14 @@ def test_vectorizers_invalid_ngram_range(vec):
             ValueError, message, vec.transform, ["good news everyone"])
 
 
+def _check_stop_words_consistency(estimator):
+    stop_words = estimator.get_stop_words()
+    tokenize = estimator.build_tokenizer()
+    preprocess = estimator.build_preprocessor()
+    return estimator._check_stop_words_consistency(stop_words, preprocess,
+                                                   tokenize)
+
+
 @fails_if_pypy
 def test_vectorizer_stop_words_inconsistent():
     if PY2:
@@ -1135,11 +1144,44 @@ def test_vectorizer_stop_words_inconsistent():
         vec.set_params(stop_words=["you've", "you", "you'll", 'AND'])
         assert_warns_message(UserWarning, message, vec.fit_transform,
                              ['hello world'])
+        # reset stop word validation
+        del vec._stop_words_id
+        assert _check_stop_words_consistency(vec) is False
 
     # Only one warning per stop list
     assert_no_warnings(vec.fit_transform, ['hello world'])
+    assert _check_stop_words_consistency(vec) is None
 
     # Test caching of inconsistency assessment
     vec.set_params(stop_words=["you've", "you", "you'll", 'blah', 'AND'])
     assert_warns_message(UserWarning, message, vec.fit_transform,
                          ['hello world'])
+
+
+@fails_if_pypy
+@pytest.mark.parametrize('Estimator',
+                         [CountVectorizer, TfidfVectorizer, HashingVectorizer])
+def test_stop_word_validation_custom_preprocessor(Estimator):
+    data = [{'text': 'some text'}]
+
+    vec = Estimator()
+    assert _check_stop_words_consistency(vec) is True
+
+    vec = Estimator(preprocessor=lambda x: x['text'],
+                    stop_words=['and'])
+    assert _check_stop_words_consistency(vec) == 'error'
+    # checks are cached
+    assert _check_stop_words_consistency(vec) is None
+    vec.fit_transform(data)
+
+    class CustomEstimator(Estimator):
+        def build_preprocessor(self):
+            return lambda x: x['text']
+
+    vec = CustomEstimator(stop_words=['and'])
+    assert _check_stop_words_consistency(vec) == 'error'
+
+    vec = Estimator(tokenizer=lambda doc: re.compile(r'\w{1,}')
+                                            .findall(doc),
+                    stop_words=['and'])
+    assert _check_stop_words_consistency(vec) is True
diff --git a/sklearn/feature_extraction/text.py b/sklearn/feature_extraction/text.py
index 9d8c9bc2aa8b5..6120c1d4a8f3a 100644
--- a/sklearn/feature_extraction/text.py
+++ b/sklearn/feature_extraction/text.py
@@ -270,8 +270,22 @@ def get_stop_words(self):
         return _check_stop_list(self.stop_words)
 
     def _check_stop_words_consistency(self, stop_words, preprocess, tokenize):
+        """Check if stop words are consistent
+
+        Returns
+        -------
+        is_consistent : True if stop words are consistent with the preprocessor
+                        and tokenizer, False if they are not, None if the check
+                        was previously performed, "error" if it could not be
+                        performed (e.g. because of the use of a custom
+                        preprocessor / tokenizer)
+        """
+        if id(self.stop_words) == getattr(self, '_stop_words_id', None):
+            # Stop words are were previously validated
+            return None
+
         # NB: stop_words is validated, unlike self.stop_words
-        if id(self.stop_words) != getattr(self, '_stop_words_id', None):
+        try:
             inconsistent = set()
             for w in stop_words or ():
                 tokens = list(tokenize(preprocess(w)))
@@ -281,10 +295,16 @@ def _check_stop_words_consistency(self, stop_words, preprocess, tokenize):
             self._stop_words_id = id(self.stop_words)
 
             if inconsistent:
-                warnings.warn('Your stop_words may be inconsistent with your '
-                              'preprocessing. Tokenizing the stop words '
-                              'generated tokens %r not in stop_words.' %
-                              sorted(inconsistent))
+                warnings.warn('Your stop_words may be inconsistent with '
+                              'your preprocessing. Tokenizing the stop '
+                              'words generated tokens %r not in '
+                              'stop_words.' % sorted(inconsistent))
+            return not inconsistent
+        except Exception:
+            # Failed to check stop words consistency (e.g. because a custom
+            # preprocessor or tokenizer was used)
+            self._stop_words_id = id(self.stop_words)
+            return 'error'
 
     def build_analyzer(self):
         """Return a callable that handles preprocessing and tokenization"""