After a brief professional basketball career, Flynn worked in several fields, including as a high school teacher and a probation officer, before entering politics.

As a city councilor, Flynn stood in opposition to rate increases by utility companies and regularly proposed tenants' rights ordinances.

[8] The Nationals relocated to Philadelphia to become the 76ers, but Flynn did not play for them, as he spent part of the 1963–64 season with the Wilmington Blue Bombers of the Eastern Professional Basketball League.

[2][16] In 1973, he worked against implementing the city of Boston's desegregation school busing plan even filing a lawsuit against the Massachusetts Board of Education over the matter.

Flynn refused to join the militant anti-busers, Louise Day Hicks and William Bulger when they released a statement of resistance that was seen as having racist overtones.

[17][21] The law was undercut in 1981, when the Massachusetts Supreme Judicial Court held that women with Medicaid eligibility had a constitutionally-protected entitlement to receive funding through the program for their abortions.

[1] Peter Dreier would later describe Flynn as having transitioned as a city councilor, "from a parochial neighborhood politician with progressive leanings to a crusader with citywide appeal.

He supported the idea of implementing linkage fees that would require those developing large projects to provide a percentage of money to affordable housing.

[38] Flynn was an outspoken critic of the cuts that President Ronald Reagan championed making to federal revenue sharing, urban development grants, and housing and job assistance programs.

[48][49] The bill was ultimately incorporated into the broader Cranston-Gonzales National Affordable Housing Act, which was passed by the U.S. Congress and signed into law by President George H. W. Bush in October 1990.

[48] In 1989, two studies, including one by the Boston Redevelopment Authority, found the city's major banks to be discriminating in practices regarding mortgage lending, personnel hiring, and where they located their branches.

[2] Flynn heeded the advice of this advisory committee, and "opened the books" on the city's fiscal situation, something that his immediate predecessor, Kevin White, had refused to do himself.

[2] In 1990, Flynn received strong criticism from Black leaders over the city police's handling of the investigation into the murder of Carol Stuart, including the arrest and intensive search of William Bennett.

[60] In response to concerns over the police department (including those stemming from the investigation into Carol Stuart's murder), in May 1991, Flynn empaneled the St. Clair Commission, headed by James D. St.

[31] In January 1992, the St. Clair Commission released its report, which was critical of the Boston Police Department for mismanagement, and urged against reappointing Commissioner Roache when his term expired that April.

[61] Retrospectively, in 2023 Michael Jonas of Commonwealth magazine wrote that, as mayor, Flynn went "to great lengths to promote racial harmony and heal divisions, not inflame them.

"[62] In 1993, George B. Merry observed, While it would be a mistake to suggest Boston has been free of racial tensions during Flynn's years as mayor, his leadership has addressed the needs of minorities, including not only blacks but the fast-growing Hispanic and Asian populations.

[63] Peter Dreier would describe Flynn as having been elected "with a populist mandate to 'share the prosperity' of Boston's downtown economic boom—particularly in terms of jobs and housing—with the city's poor and working-class residents."

[2][24] After a five-year campaign by Flynn and community activists, United States Secretary of Housing and Urban Development Samuel Pierce agreed to hand over to community-based non profits and tenant organizations a total of 2,000 HUD-subsidized apartments located in roughly 70 buildings that had been abandoned by property owners.

[24] Boston's development director Steve Coyle oversaw the institution of controversial "downzoning" growth management safeguards aimed at combatting the "Manhattanization" of the city's historic downtown and neighborhoods.

[72] The article included a reporter's claim to have, firsthand, witnessed Flynn walking around Boston while seemingly drunk while visiting the city on break from his ambassadorial duties on August 6, 1997.

[77] However, obstacles, such as a lack of financial campaign reserves and the political challenge of running for governor in the state of Massachusetts with a strong anti-abortion stance like his, dissuaded him.

[32] Another factor that made his candidacy challenging was the perceived difficulty of winning statewide with a political identity so strongly tied to the city of Boston.

[80] Flynn was the only anti-abortion candidate of the ten running in the primary, and his campaign advertising utilized photos of him with Pope John Paul II and Mother Teresa.

Ceci Connolly of The Washington Post observed during the campaign, In this era of "third way," suburban, New Democrat politics, Flynn's New Deal, patronage-oriented, urban populism may have outgrown its welcome even here in the bosom of liberalism.

[32]In 2001, for several weeks Flynn openly explored a possible run in that year's special election to succeed Joe Moakley as the congressman from Massachusetts's 9th congressional district.

However, in mid-June 2001, Flynn ruled out such a run and threw his support behind a potential candidacy by State Senator Stephen Lynch,[81] who ultimately ran and won the election.

[85] In 2010, Flynn again crossed party lines to vote for the successful candidacy of Republican nominee Scott Brown for the United States Senate.

[113] In May 2007, Flynn joined the College of Fellows of the Dominican School of Philosophy and Theology in Berkeley, California, who also awarded him the honorary degree Doctor of Humane Letters.

[115] In March 2011, Flynn's home was broken into; among the valuables taken were rosary beads blessed by Pope John Paul II and letters from influential world figures.