Clemons suffered a stroke in June 2011. He underwent two surgeries, after which he was declared to be in serious but stable condition. According to Rolling Stone magazine, he had been showing signs of recovery. However, on June 18, 2011, he died from complications caused by the stroke while in West Palm Beach, Florida. He was 69. Upon announcement of Clemons' death, New Jersey Governor Chris Christie ordered all state flags to be lowered to half staff in his honor. He was survived by his four sons and his fifth wife, Victoria, whom he had married in 2008.
At their concert in Portsmouth, Virginia, on June 19, 2011, Phish covered "Thunder Road" as a tribute to Clemons.
At an Eddie Vedder concert in Hartford, Connecticut on June 18, 2011, Vedder wished Clemons well, and was soon notified by a sound tech that Clemons had died. Vedder later played a tribute to Clemons during Pearl Jam song "Better Man" changing the lyrics to include, "Can't find a Bigger Man" (paying homage to Clemons' nickname "The Big Man"). During a subsequent performance on the Late Show with David Letterman, Vedder played a ukulele with "Clarence" written across the front of it.
Before singing "Moment of Surrender" at the U2 concert in Anaheim on June 18, 2011, Bono paid tribute to Clemons. He read lyrics from Springsteen's "Jungleland" near the end of the song, and repeated them at the song's conclusion. Bono repeated this dedication and tribute during "Moment of Surrender" at the U2 concert in New Jersey on June 21 and again in Baltimore on June 22.
Bon Jovi performed "Tenth Avenue Freeze-Out" as the first encore during their concert in Horsens on June 19, 2011. While playing that song, photos of Clemons were shown on the giant video screen behind the band.
Jimmy Buffett added verses that included Clemons in "The Stories We Could Tell" during his final encore during his concert on June 21, 2011. The rest of the band left the stage and it was Buffett playing and singing alone.
On July 17, 2011, a tribute concert was held at the Wonder Bar in Asbury Park, New Jersey. Springsteen performed a 45-minute set playing some of Clemons' songs. Clemons' son, Clarence III, (known as Nick), opened the show with his band, The Nick Clemons Band.
On October 1, 2011, a tribute to Clemons took place at the Seminole Hard Rock Hotel and Casino in Hollywood, Florida. Traditionally an annual charity event hosted by Clemons called The Classic Rock & Roll Party, the event paid tribute to Clemons' life and all he did for Home Safe, a non-profit organization helping victims of child abuse and domestic violence.
In October 2011 Lady Gaga paid tribute to him when she accepted the "Big Man of the Year" from Little Kids Rock. In a June 21, 2012 concert in Sydney, Australia Gaga dedicated her song "The Edge of Glory" in which Clemons has contributed.