diff --git a/build_tools/travis/flake8_diff.sh b/build_tools/travis/flake8_diff.sh
index 84495b339a922..9781f7e6a5cc0 100755
--- a/build_tools/travis/flake8_diff.sh
+++ b/build_tools/travis/flake8_diff.sh
@@ -137,12 +137,9 @@ check_files() {
 if [[ "$MODIFIED_FILES" == "no_match" ]]; then
     echo "No file outside sklearn/externals and doc/sphinxext/sphinx_gallery has been modified"
 else
-    # Default ignore PEP8 violations are from flake8 3.3.0
-    DEFAULT_IGNORED_PEP8=E121,E123,E126,E226,E24,E704,W503,W504
-    check_files "$(echo "$MODIFIED_FILES" | grep -v ^examples)" \
-           --ignore $DEFAULT_IGNORED_PEP8
-    # Examples are allowed to not have imports at top of file
+
+    check_files "$(echo "$MODIFIED_FILES" | grep -v ^examples)"
     check_files "$(echo "$MODIFIED_FILES" | grep ^examples)" \
-           --ignore $DEFAULT_IGNORED_PEP8 --ignore E402
+        --config ./examples/.flake8
 fi
 echo -e "No problem detected by flake8\n"
diff --git a/examples/.flake8 b/examples/.flake8
new file mode 100644
index 0000000000000..703bf15e79bff
--- /dev/null
+++ b/examples/.flake8
@@ -0,0 +1,5 @@
+# Examples specific flake8 configuration
+
+[flake8]
+# Same ignore as project-wide plus E402 (imports not at top of file)
+ignore=E121,E123,E126,E24,E226,E704,W503,W504,E402
diff --git a/setup.cfg b/setup.cfg
index 378905311e17e..02b3015e87f2e 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -38,6 +38,10 @@ artifact_indexes=
     # https://ci.appveyor.com/project/sklearn-ci/scikit-learn/
     http://windows-wheels.scikit-learn.org/
 
+[flake8]
+# Default flake8 3.5 ignored flags
+ignore=E121,E123,E126,E226,E24,E704,W503,W504
+
 # Uncomment the following under windows to build using:
 # http://sourceforge.net/projects/mingw/