diff --git a/hgext/mq.py b/hgext/mq.py
--- a/hgext/mq.py
+++ b/hgext/mq.py
@@ -1575,8 +1575,18 @@ class queue(object):
             m = list(mm)
             r = list(dd)
             a = list(aa)
-            c = [filter(matchfn, l) for l in (m, a, r)]
-            match = scmutil.matchfiles(repo, set(c[0] + c[1] + c[2] + inclsubs))
+
+            # create 'match' that includes the files to be recommited.
+            # apply matchfn via repo.status to ensure correct case handling.
+            cm, ca, cr, cd = repo.status(patchparent, match=matchfn)[:4]
+            allmatches = set(cm + ca + cr + cd)
+            refreshchanges = [x.intersection(allmatches) for x in (mm, aa, dd)]
+
+            files = set(inclsubs)
+            for x in refreshchanges:
+                files.update(x)
+            match = scmutil.matchfiles(repo, files)
+
             bmlist = repo[top].bookmarks()
 
             try:
@@ -1656,6 +1666,7 @@ class queue(object):
                 n = newcommit(repo, oldphase, message, user, ph.date,
                               match=match, force=True)
                 # only write patch after a successful commit
+                c = [list(x) for x in refreshchanges]
                 if inclsubs:
                     self.putsubstate2changes(substatestate, c)
                 chunks = patchmod.diff(repo, patchparent,
diff --git a/tests/test-casefolding.t b/tests/test-casefolding.t
--- a/tests/test-casefolding.t
+++ b/tests/test-casefolding.t
@@ -160,4 +160,15 @@ case changes.
   $ hg status -A
   C MiXeDcAsE
 
+  $ hg qpop -a
+  popping refresh-casechange
+  patch queue now empty
+  $ hg qnew refresh-pattern
+  $ hg status
+  $ echo A > A
+  $ hg add
+  adding A
+  $ hg qrefresh a # issue 3271, qrefresh with file handled case wrong
+  $ hg status # empty status means the qrefresh worked
+
   $ cd ..
diff --git a/tests/test-mq-qrefresh.t b/tests/test-mq-qrefresh.t
--- a/tests/test-mq-qrefresh.t
+++ b/tests/test-mq-qrefresh.t
@@ -208,6 +208,7 @@ qrefresh --short tests:
   $ echo 'orphan' > orphanchild
   $ hg add orphanchild
   $ hg qrefresh nonexistentfilename # clear patch
+  nonexistentfilename: No such file or directory
   $ hg qrefresh --short 1/base
   $ hg qrefresh --short 2/base