Timoney took the captain's exam in January 1985 and was promoted in the summer of that year and assigned as the executive officer of the 48th Precinct. He did not get along with the commanding officer there, but a quick transfer opportunity brought him to the 14th Precinct (Midtown South). There, he handled several high-profile issues, including a focus on cleaning up quality-of-life crimes in Bryant Park and overseeing security for the 40th anniversary United Nations General Assembly. After ten months as 14th Precinct Executive Officer, he was made Commanding Officer of the 5th Precinct (Chinatown, Little Italy and Lower East Side), which was considered an assignment for high-potential NYPD leaders. In September 1987, Timoney was transferred again, this time to police headquarters, as Commanding Officer of the Chief of Department's Office (under Deputy Chief Tom Walsh).