In 1994, he became the youngest person in NYPD history to be named Chief of Department (the top ranking uniformed/sworn officer, essentially third in command, similar to a large corporate COO). He ultimately served as Commissioner Bill Bratton's First Deputy Commissioner, making him the second man in the force. In 1996, Bratton left the department because of conflicts with Mayor Rudy Giuliani. Timoney criticized Bratton's replacement, Howard Safir, as a "lightweight" and retired later the same year, having served for a total of 28 years. Afterwards, he worked as a consultant to local police forces and various government programs.