He served in the United States Army Air Corps from 1943 to 1946 during World War II, reaching the rank of Captain.

Throughout most of his tenure as mayor, Flaherty successfully opposed the Early Action Program, a project which included the development of Skybus.

At the end of his tenure, the dispute over this program was resolved by a study performed through the agreement of Flaherty, the county commissioners, representatives of labor and the City Council.

He was criticized in the African-American community for opposing busing desegregation, and he dismantled the existing majority-black Freedom House Ambulance Service in favor of a new, predominantly white city paramedic system, an action which some attributed to the mayor's racism.

[8] One of his early appointments was former Duquesne University and Boston Celtics basketball star Chuck Cooper, as Director of Parks and Recreation.

[citation needed] Flaherty was a prominent supporter of Jimmy Carter during the 1976 United States presidential election.

[12] He supported longtime commissioner and fellow Democrat Tom Foerster's long-term goal of building a world class airport in Allegheny County.

The team of Foerster as chairman and Pete Flaherty as the second Democrat on the three-member Board of County Commissioners served together for three four year terms.