Dan Prescott, 31, of Hagerstown, was driving his Pontiac Grand Am north on Summit Avenue and Flanagan was driving his marked car west on Antietam Street when the crash occurred, police said.
Both cars ended up near the northwest corner of the intersection.
The Pontiac crossed over the sidewalk, scraping its right side along a utility pole at the corner and coming to rest against a building. The airbag deployed.
The patrol car came to rest on Summit Avenue.
Prescott was wearing a cast on one foot, which he said was the result of a racquetball injury.
"It's just not been a good month," Prescott said.
This is the second accident involving a city police cruiser since March 29, when a patrol car with its lights and sirens on and another vehicle collided at the intersection of North Mulberry and East Washington streets.
In the March accident, Hagerstown Police Chief Arthur Smith said Officer Charles Streightiff was driving on North Mulberry Street when the patrol car and a vehicle driven east on East Washington Street collided.
Streightiff suffered only minor scrapes and bruises, Smith said at the time.