He was one of three Congress of Racial Equality (CORE) field workers murdered in rural Neshoba County, Mississippi, by members of the Ku Klux Klan.

Schwerner and two co-workers, James Chaney and Andrew Goodman, were killed in response to their civil rights work, which included promoting voting registration among African Americans, most of whom had been disenfranchised in the state since 1890.

His mother, Anne Siegel (May 1, 1912 – November 29, 1996), was a science teacher at nearby New Rochelle High School, and his father, Nathan Schwerner (June 19, 1909 – March 6, 1991), was a businessman.

[7] The Ku Klux Klan targeted Schwerner after he and his wife, Rita, had taken over the Meridian CORE field office, where they established a community center for blacks as part of grassroots organizing.

The Sheriff's Deputy, Cecil Price, had been accused by parishioners of stopping their caravan and forcing the deacons to kneel in the headlights of their own cars, while they were beaten with rifle butts.

Deputy Sheriff Cecil Price arrested Chaney, Goodman, and Schwerner for an alleged traffic violation and took them to the jail in Neshoba County.

On the way back to Meridian, they were stopped by patrol lights and two carloads with members of the White Knights of the Ku Klux Klan on Highway 19, then taken in Price's car to another remote rural road.

One of the Klansmen, Alton Wayne Roberts, reportedly pulled Schwerner out of the car, pointed a gun at his chest, and asked "Are you that nigger lover?".

Journalist Jerry Mitchell, an award-winning investigative reporter for the Jackson Clarion-Ledger had written extensively about the case for many years in the late 20th century.

Mitchell had earned renown for helping secure convictions by his investigation of several other high-profile Civil Rights Era murder cases, including the assassination of Medgar Evers in Mississippi, the 1963 16th Street Baptist Church bombing in Birmingham, and the murder of Vernon Dahmer in his Mississippi home, the latter of which was ordered by Samuel Bowers, founder of the Klan chapter that killed the CORE activists.

Barry Bradford, an Illinois high school teacher, and three students: Allison Nichols, Sarah Siegel, and Brittany Saltiel, joined Mitchell's efforts.

On January 7, 2005, Edgar Ray Killen, an outspoken white supremacist nicknamed "Preacher," pleaded "Not Guilty" to state charges of the murders of the three men.

"[10] Robert Reich, the American political commentator, professor, and author who served in the administrations of Presidents Gerald Ford, Jimmy Carter, and Bill Clinton, says that as a child, he was bullied, and sought out the protection of older boys; one of them was Michael Schwerner.