He died of a heart attack in Yosemite Valley, California, on July 6, 1901, right before the Sierra Club's first High Trip. The Sierra Club built the LeConte Memorial Lodge in his honor in 1904. The Le Conte Glacier, Le Conte Canyon, Le Conte Divide, Le Conte Falls and Mount Le Conte were named after him. LeConte Hall, which houses the Department of History at the University of Georgia, was named for him and his brother. LeConte College, which houses the Department of Mathematics and Statistics near the Horseshoe at the University of South Carolina, Le Conte Middle School in Hollywood, and Le Conte Avenue in Berkeley also honor the two brothers, both of whom are buried in Mountain View Cemetery in Oakland, California.