The FBI entered the case after the men disappeared. They helped find them buried in an earthen dam. The US government prosecuted the case under the Enforcement Act of 1870. The Neshoba County deputy sheriff and six conspirators were convicted by Federal prosecutors of civil rights violations but were not convicted of murder. Two defendants were acquitted because the jury deadlocked.

Schwerner had been working closely with an assistant James Chaney, also a civil rights Activist in Meridian. On the morning of June 21, 1964, the three men set out for Philadelphia, Neshoba County, where they were to investigate the recent burning of Mount Zion Methodist Church, a black church that had agreed to be a site for a religious school for education and voter registration.

In 1966, Andrew’s parents, Robert and Carolyn Goodman started The Andrew Goodman Foundation to carry on the spirit and purpose of their son’s life. After the death of Robert Goodman in 1969, Carolyn continued the work of the Foundation, focusing on projects like a reverse march to Mississippi and a 25th Anniversary Memorial. The memorial, which took place at St. John The Divine Church in NYC, was attended by 10,000 people and was presided by Governor Mario Cuomo, Maya Angelou, Peter Seeger, Aaron Henry, Harry Belafonte, Robert Kennedy Jr., and others closely associated with the Civil Rights movement. After Carolyn’s death in August 2007, David Goodman, Andrew’s younger brother, and Sylvia Golbin Goodman, David’s wife, took up the work of the Foundation.

The Mississippi State Sovereignty Commission was strongly opposed to integration and civil rights. It paid spies to identify citizens suspected of activism, especially northerners who entered the state. The records opened by court order in 1998 also revealed the state's deep complicity in the murders of Chaney, Goodman, and Schwerner, because its investigator A. L. Hopkins passed on to the Commission information about the workers, including the car license number of a new civil rights worker. Records showed the Commission, in turn, passed on the information to the Neshoba County Sheriff, who was implicated in the murders.

On 14 September 2004, Mississippi State Attorney General Jim Hood announced that he was gathering evidence for a charge of murder and intended to take the case to a grand jury. On 7 January 2005, Edgar Ray Killen was arrested. He was found guilty of three counts of manslaughter — not murder — on June 21, 2005, exactly 41 years to the day after the murders. He was sentenced to sixty years in prison—twenty years for each count, to be served consecutively.

For nearly 50 years, the organization was a private foundation acting in the public interest. With their eyes set on the Future, the Board of Trustees of The Andrew Goodman Foundation elected to turn the organization into a public charity in 2012. In 2014, on the fiftieth anniversary of the murders, the Foundation officially launched Vote Everywhere, a program designed to support college students who are continuing the work of Freedom Summer.

Andrew Goodman was born and raised in the Upper West Side of New York City, at 161 West 86 Street. He was the second of three boys born of Robert and Carolyn Goodman, and, like fellow murdered Activist Michael Schwerner, was Jewish. His family and community were steeped in intellectual and socially progressive activism and were devoted to social justice. An Activist at an early age, Goodman graduated from the progressive Walden School, which was said to have had a strongly formative influence on his outlook. He attended the Honors Program at the University of Wisconsin–Madison for a semester but withdrew after falling ill with pneumonia.

On June 20, 2016, just one day ahead of the 52nd anniversary of the murders, Attorney General Hood announced an end to the federal and state investigations into the 'Mississippi Murders', officially closing the case.

Bradford and his students’ documentary, produced for the National History Day contest, presented important new evidence and compelling reasons for reopening the Goodman, Chaney, and Schwerner case. They also obtained an interview with Edgar Ray Killen, which helped persuade the state to open the case for investigation. Mitchell was able to determine the identity of "Mr. X", the mystery informer who had helped the FBI discover the bodies and smash the conspiracy of the Klan in 1964, in part using evidence developed by Bradford and the students.