Screening for Aviation Command, he served as Executive Officer and later Commanding Officer of Tactical Electronic Warfare Squadron THIRTY-THREE (VAQ-33) at NAS Key West, Florida within the Fleet Electronic Warfare Support Group.

He then served as Air Officer aboard the USS America (CV-66) followed by shore duty as a special assistant to the Chief of Naval Operations.

Penn retired from the Navy in the rank of Captain and entered the private sector in 1995, joining Loral Corporation as Director of International Business; his work at Loral focused on airborne Electronic Warfare and Defensive Electronic Counter Measure Systems.

In 1998, he transferred to the Lockheed Martin's Naval Electronics and Surveillance Systems working Advanced Programs; there he focused on Interoperability CONOPS for the Joint Strike Fighter Program, on upgrading the technology used in the F-16 Fighting Falcon, on efforts to develop Unmanned Aerial Vehicles and Autonomous Undersea Vehicles, and on C4ISR initiatives.

Under President Barack Obama, he briefly served as acting United States Secretary of the Navy from March 13, 2009[1] to May 19, 2009.