Director Mark Pellington won the MTV Video Music Award for Best Direction in 1993 for his direction of the video.
Due to the major success of the music video, Pearl Jam began to feel that the video overshadowed the song. Bassist Jeff Ament stated, "Ten years from now, I don't want people to remember our songs as videos." Since "Jeremy," Pearl Jam has rarely produced music videos except for "Do the Evolution" (1998), "I Am Mine," (2002), "Save You" (2002), "World Wide Suicide" (2006), "The Fixer" (2009) and "Sirens" (2013).
The violent imagery of the music video led MTV to impose censorship of the video, specifically altering the shot of Jeremy's character placing a gun into his mouth by zooming into the shot. The uncut version keeps the original, unaltered shot in. The uncut version has only been aired on rare occasions on MTV, and always after a certain hour late in the evening.
In 1996, a shooting occurred at Frontier Junior High School in Moses Lake, Washington that left three dead and a fourth injured. The prosecutors for the case said shooter, Barry Loukaitis, was influenced by the edited version of the music video. Loukaitis' inspiration was based on a misconception as Jeremy never shot any of his classmates in the video.
After the 1999 Columbine High School shooting, MTV rarely aired the video and any mention of it was omitted in retro-documentaries such as "I Love the '90s."