In addition to his scientific accomplishments, Julian was a social activist. He was involved in several groups to improve conditions for African-Americans, and helped found the Legal Defense and Educational Fund of Chicago. He also founded the Julian Research Institute in 1964, a nonprofit organization that he ran for the rest of his life. In 1973, he was the first black chemist elected to the National Academy of the Sciences.

Julian died of liver cancer in 1975. In 1980, DePauw University rededicated a building as the Percy L. Julian Science and Mathematics Center. In 1990, he was elected to the National Inventors Hall of Fame, and in 1999 his creation of a glaucoma treatment was recognized by the American Chemical Society as "one of the top 25 achievements in the history of American chemistry." The PBS series Nova created a documentary of his life, he was rewarded with a stamp issued by the U.S. Postal Service, and Google honored him with a Doodle.