Hooper died at the age of 87 in Santa Cruz, California. He had been healthy enough to attend that summer's Baseball Hall of Fame induction ceremonies and he had gone duck hunting less than a month before he died. Hooper had surgery for a circulatory issue three weeks before his death, but he seemed to have recovered well from that procedure. Harry Hooper Jr said that Hooper had died of old age. He said that Hooper was the oldest living member of the Hall of Fame before his death.