diff --git a/CHANGES b/CHANGES
index a753d9d99..a84fbd717 100644
--- a/CHANGES
+++ b/CHANGES
@@ -15,6 +15,8 @@ Bugs fixed
 
 * #3445: setting ``'inputenc'`` key to ``\\usepackage[utf8x]{inputenc}`` leads
   to failed PDF build
+* EPUB file has duplicated ``nav.xhtml`` link in ``content.opf``
+  except first time build
 
 Testing
 --------
diff --git a/sphinx/builders/epub.py b/sphinx/builders/epub.py
index c22f5ff76..0aae00a0f 100644
--- a/sphinx/builders/epub.py
+++ b/sphinx/builders/epub.py
@@ -570,7 +570,7 @@ class EpubBuilder(StandaloneHTMLBuilder):
         self.ignored_files = ['.buildinfo', 'mimetype', 'content.opf',
                               'toc.ncx', 'META-INF/container.xml',
                               'Thumbs.db', 'ehthumbs.db', '.DS_Store',
-                              self.config.epub_basename + '.epub'] + \
+                              'nav.xhtml', self.config.epub_basename + '.epub'] + \
             self.config.epub_exclude_files
         if not self.use_index:
             self.ignored_files.append('genindex' + self.out_suffix)