He was born and raised in New York City, he enrolled at Queens College, New York City, around 1958 and was a classmate of Paul Simon (musician). In 1964 he volunteered, along with fellow activist Mickey Schwerner, to work as part of the "Freedom Summer" project to register blacks to vote in Mississippi. He was trained, along with Schwerner, at a site in the northern United States. In mid-June of 1964 Goodman and Schwerner were sent to Mississippi and begin to register blacks to vote, and on the night of June 20, 1964 the two reached Meridian. There, they were joined by a black man named James Cheney, who himself was a civil rights activist. On the morning of June 21, 1964 the three of them set out for Neshoba County, where they were to investigate a recent burning of a black church. At some point, they were stopped by members of the Ku Klux Klan, including the Neshoba County sheriff, after which they were beaten and shot to death. His body was found on August 4.
Eventually the Neshoba County sheriff and conspriators were convicted by Federal prosecutors of civil rights violations, but were never convicted of murder. The case formed the basis of the film Mississippi Burning.