Doug Lynch had initially been placed on leave Wednesday from his post as vice dean of Penn's Graduate School of Education.
On Thursday, he resigned from the Ivy League university in Philadelphia.
There are reports that some faculty and staff learned months ago that Lynch never received his degree from Columbia University.
The university at first said it had sanctioned Lynch while allowing him to stay in his position. School officials later announced he'd been placed on leave.
A spokesman for the graduate school said Lynch mistakenly believed his degree was complete.
