Kennedy was born on November 11, 1962, in Sault Ste. Marie, Michigan. He earned a Bachelor of Science degree in chemistry at the University of Florida in 1984 and a Ph.D. from the University of North Carolina-Chapel Hill (UNC) in 1988 while working under James Jorgenson. He was an NSF post-doctoral fellow at UNC from 1989-1991 with R. Mark Wightman.