diff --git a/mercurial/repair.py b/mercurial/repair.py
--- a/mercurial/repair.py
+++ b/mercurial/repair.py
@@ -134,6 +134,8 @@ def strip(ui, repo, nodelist, backup="al
             for i in xrange(offset, len(tr.entries)):
                 file, troffset, ignore = tr.entries[i]
                 repo.sopener(file, 'a').truncate(troffset)
+                if troffset == 0:
+                    repo.store.markremoved(file)
             tr.close()
         except: # re-raises
             tr.abort()
diff --git a/mercurial/store.py b/mercurial/store.py
--- a/mercurial/store.py
+++ b/mercurial/store.py
@@ -343,6 +343,9 @@ class basicstore(object):
     def invalidatecaches(self):
         pass
 
+    def markremoved(self, fn):
+        pass
+
     def __contains__(self, path):
         '''Checks if the store contains path'''
         path = "/".join(("data", path))
@@ -421,6 +424,15 @@ class fncache(object):
             self._dirty = True
             self.entries.add(fn)
 
+    def remove(self, fn):
+        if self.entries is None:
+            self._load()
+        try:
+            self.entries.remove(fn)
+            self._dirty = True
+        except KeyError:
+            pass
+
     def __contains__(self, fn):
         if self.entries is None:
             self._load()
@@ -495,6 +507,9 @@ class fncachestore(basicstore):
     def invalidatecaches(self):
         self.fncache.entries = None
 
+    def markremoved(self, fn):
+        self.fncache.remove(fn)
+
     def _exists(self, f):
         ef = self.encode(f)
         try:
diff --git a/tests/test-strip.t b/tests/test-strip.t
--- a/tests/test-strip.t
+++ b/tests/test-strip.t
@@ -336,6 +336,19 @@ 2 different branches and a common ancest
   saved backup bundle to $TESTTMP/test/.hg/strip-backup/*-backup.hg (glob)
   $ restore
 
+verify fncache is kept up-to-date
+
+  $ touch a
+  $ hg ci -qAm a
+  $ cat .hg/store/fncache | sort
+  data/a.i
+  data/bar.i
+  $ hg strip tip
+  0 files updated, 0 files merged, 1 files removed, 0 files unresolved
+  saved backup bundle to $TESTTMP/test/.hg/strip-backup/*-backup.hg (glob)
+  $ cat .hg/store/fncache
+  data/bar.i
+
 stripping an empty revset
 
   $ hg strip "1 and not 1"