Following his retirement from the FBI in 1998, Noonan was appointed as Northeast Regional Director for the Attorney General's Bureau of Narcotics Investigation.
After 11 years as Regional Director, Noonan was promoted to Chief of Criminal Investigations for the Office of Attorney General in July 2009.
On January 18, 2011 Noonan was appointed as the commissioner of the Pennsylvania State Police by Governor Tom Corbett.
Noonan became a national household name after speaking at daily press conferences after the shooting and during the subsequent man hunt for Eric Frein.
On September 14, two days after the attack Noonan asked for additions man power and assets from state police agencies in New York and New Jersey.