John Joseph Connolly Jr. (born August 1, 1940) is an American former FBI agent who was convicted of racketeering, obstruction of justice and murder charges stemming from his relationship with Boston mobsters James "Whitey" Bulger, Steve Flemmi and the Winter Hill Gang.

State and federal authorities had been trying to imprison Bulger for years, but he evaded capture until 2011. As the FBI handler for Bulger and Flemmi, Connolly (who was previously neighbors with Bulger's family in the Old Harbor Housing Project) had been protecting them from prosecution by supplying Bulger with information about possible attempts to catch them. Connolly was indicted on December 22, 1999, on charges of alerting Bulger and Flemmi to investigations, falsifying FBI reports to cover their crimes and accepting bribes.

In 2000, Connolly was charged with additional racketeering-related offenses. He was convicted in 2002 and sentenced to ten years in federal prison. In 2008, he was convicted on state charges of second-degree murder in Florida and sentenced to forty years in prison. He was released from federal prison on June 28, 2011, and transferred to the Florida State Prison to serve the remainder of his sentence for his 2008 conviction.

In April 2020, Connolly asked to be allowed to serve the remainder of his sentence on home confinement due to fears of contracting COVID-19, citing a 2018 federal law allowing for compassionate release under "extraordinary" circumstances, such as age, health and other critical factors. A Florida judge initially declined to order his release, but Connolly was later granted a medical release on February 17, 2021.