Born in Boston in 1935 to an Irish Catholic family, John Joseph Geoghan attended local parochial schools. Intending to become a priest, he attended Cardinal O'Connell Seminary. An assessment in 1954 noted him as "markedly immature." He graduated in 1962 and was ordained.

On February 13, 1962 Geoghan was assigned as an assistant pastor at Blessed Sacrament Parish in Saugus, Massachusetts. That December, Geoghan successfully talked a man out of committing suicide by jumping off the Mystic River Bridge. While Geoghan was assigned to Blessed Sacrament, Rev. Anthony Benzevich allegedly told church officials that the junior priest was observed bringing boys into his bedroom. Benzevich would later deny this allegation. In 1998, Benzevich told reporters he was branded as a troublemaker for reporting Geoghan, and that church officials hinted that he might be sent to Peru if he persisted. In 1995 Geoghan admitted to having molested four boys during his tenure in Saugus.

Geoghan was assigned to St. Bernard's Parish in Concord starting on September 22, 1966. He was transferred after seven months there; church records offered no explanation for his reassignment.

On April 20, 1967, Geoghan was assigned to St. Paul's Parish in Hingham. Around 1968, a man complained to church authorities that he had caught Geoghan molesting his son. As a result, Geoghan was sent to the Seton Institute in Baltimore for treatment for his pedophilia. In the early 1970s, parishioner Joanne Mueller accused Geoghan of molesting her four young sons. Mueller has said that she informed Rev. Paul E. Miceli and he asked her to keep quiet. Miceli disputes her account. The church later reached a settlement with Mueller.

Geoghan's next assignment was at St. Andrew's Parish in Boston's Jamaica Plain neighborhood, starting on June 4, 1974. On February 9, 1980 Rev. John E. Thomas told Bishop Thomas Vose Daily that Geoghan admitted to molesting seven boys. Daily called Geoghan and told him to go home. Geoghan admitted to the abuse, but said that he did "not feel it serious or a pastoral Problem." He was placed on sick leave three days later and ordered by Cardinal Humberto Medeiros to undergo counseling. Under the care of doctors Robert Mullins and John H. Brennan, Geoghan underwent psychoanalysis and psychotherapy.

On February 25, 1981, Geoghan returned to pastoral work at St. Brendan's Parish in Dorchester. While there, he allegedly raped and fondled a boy. In 1982 the family of seven of Geoghan's victims complained to Bishop Daily that Geoghan had arranged to meet one of his victims at an ice cream shop in Jamaica Plain and was at the time in the company of another boy. On September 18, 1984, Cardinal Bernard Francis Law, the new archbishop of Boston, removed Geoghan from the parish after complaints that he was molesting children.

On November 13, 1984, Law assigned Geoghan to St. Julia's Parish in Weston. He was put in charge of three youth groups, including altar boys. On December 7, 1984, Auxiliary Bishop John Michael D'Arcy wrote to Law complaining about Geoghan's assignment to St. Julia's because of his "history of homosexual involvement with young boys." That same month, Mullins wrote that Geoghan had "fully recovered," and Brennan stated that there was no need for restrictions on his work as a priest.

John Michael D'Arcy, who had written an unheeded letter of warning to Cardinal Law about Geoghan's behavior, was transferred from Boston to Indiana on February 26, 1985, and ended his career as Bishop of the Diocese of Fort Wayne–South Bend. D'Arcy retired in 2009, and died in 2013.

Robert Joseph Banks, when an auxiliary bishop in Boston, had recommended in 1989 that Geoghan remain as a parish priest despite receiving an assessment that he would likely continue to act on his pedophilia. Banks was appointed Bishop of the Diocese of Green Bay in 1990. He retired in 2003, having reached the church's mandatory retirement age of 85 years. Banks remains Bishop Emeritus of Green Bay.

On November 28, 1990, Banks recommended that Geoghan return to the parish, but left the decision up to Cardinal Law and another bishop. On October 23, 1991 the church received a complaint about Geoghan "proselytizing" with a boy at a pool.

Over a 30-year career in six parishes, Geoghan was accused of sexual abuse involving more than 130 boys. He was prosecuted in Cambridge, Massachusetts for charges of molestation that took place in 1991. Geoghan was defrocked in 1998 by Pope John Paul II. He was found guilty in January 2002 of indecent assault and battery for grabbing the buttocks of a 10-year-old boy in a swimming pool at the Waltham Boys and Girls Club in 1991, and was sentenced to nine to ten years in prison.

In 1993, Geoghan retired from active ministry at the age of 58. He moved into the Regina Cleri residence for retired Priests. Three years later, after more allegations surfaced against him, he spent several months in therapy in the Southdown Institute in Ontario, Canada.

The investigation and prosecution of Geoghan was one of numerous cases of Priests accused of sexual abuse in a scandal that rocked the archdiocese in the 1990s and 2000s. It led to the resignation of Boston's archbishop, Cardinal Bernard Francis Law, on December 13, 2002. Law lost the support of fellow clergy and the laity after it was shown that his response to allegations against dozens of Priests consisted of assigning them to different parishes, thus allowing sexual abuse of additional children to take place. Geoghan was finally convicted of sexual abuse, laicized, and sentenced in 2002 to nine to ten years in Souza-Baranowski Correctional Center, a maximum-security prison. Less than a year later, he was murdered there by Joseph Druce, an inmate who is serving a life sentence. The Boston Globe's coverage of Geoghan's abuse opened the door for public knowledge of the sexual abuse scandal in the Catholic archdiocese of Boston and sexual abuse by Priests in the United States in general. This coverage is a key plot element of the movie Spotlight that was released in 2015.

Geoghan was buried in Holyhood Cemetery in Brookline, Massachusetts on August 28, 2003.

A Worcester, Massachusetts jury found Druce guilty of first-degree murder on January 25, 2006, after the jury rejected his insanity defense. Druce was sentenced a second time to life in prison without the possibility of parole.

A video, which shows correction officers trying to open Geoghan's prison door, which Druce had wedged shut when he attacked the former priest, was released on YouTube in June 2007. Officials claim not to know how the video, recorded by the prison surveillance systems, was made public.

After Cardinal Law resigned as Boston's archbishop in December 2002, he relocated to Rome in 2004, where he served as archpriest of the Basilica of St. Mary Major, the largest Catholic Marian church in Rome. It was "commonly believed that he would live out his retirement in Rome" after he retired at age 80 in 2011. Law died in Rome on December 20, 2017.