Hillsborough and his partner Jerry Taylor had spent the evening at a restaurant. After leaving, they were followed and confronted by Cordova and three companions. The attack happened in the parking area near Hillsborough's apartment. Cordova stabbed him repeatedly while shouting a homophobic slur. Taylor survived the encounter. Cordova was arrested and charged with murder. The brutality and clear hate motivation of the attack shocked even a city accustomed to violence. Hillsborough was described by friends and colleagues as a gentle man who loved his work tending the city's gardens.

The murder occurred just two weeks after Anita Bryant's successful campaign to repeal a gay rights ordinance in Dade County, Florida. Bryant's Save Our Children campaign had used rhetoric painting gay men as threats to children and to society. San Francisco's LGBTQ community drew a direct line between Bryant's language and Cordova's knife. Supervisor Harvey Milk, who would be assassinated the following year, publicly blamed Bryant for creating the atmosphere of hostility. A memorial march for Hillsborough drew thousands. The city lowered its flags to half-staff. The murder became a catalyst for political organizing and for the movement to enact hate crime protections.

Cordova pleaded guilty to second-degree murder and was sentenced to ten years in prison. The sentence, considered lenient by many in the LGBTQ community, foreshadowed the outrage that would follow Dan White's voluntary manslaughter conviction for the murders of Moscone and Milk the next year. Hillsborough's death is remembered as a turning point in San Francisco's LGBTQ history, a moment when the community's grief and anger translated into political power. His name appears on memorial lists alongside other victims of anti-LGBTQ violence. The quiet street where he died carries no marker, but the political movement his murder helped fuel has reshaped American civil rights law.