IE apparently does not like href=""; change this to href="#" which appears to work.

sphinx/builders/html.py

@@ -641,7 +641,8 @@ class StandaloneHTMLBuilder(Builder):
                    baseuri=self.get_target_uri(pagename)):
             if not resource:
                 otheruri = self.get_target_uri(otheruri)
-            return relative_uri(baseuri, otheruri)
+            uri = relative_uri(baseuri, otheruri) or '#'
+            return uri
         ctx['pathto'] = pathto
         ctx['hasdoc'] = lambda name: name in self.env.all_docs
         ctx['customsidebar'] = self.config.html_sidebars.get(pagename)

sphinx/environment.py

@@ -930,7 +930,7 @@ class BuildEnvironment:
         """Return a TOC nodetree -- for use on the same page only!"""
         toc = self.tocs[docname].deepcopy()
         for node in toc.traverse(nodes.reference):
-            node['refuri'] = node['anchorname']
+            node['refuri'] = node['anchorname'] or '#'
         return toc
 
     def get_toctree_for(self, docname, builder, collapse):