E.C. Slipher died in Flagstaff, Arizona on August 7, 1964 at the age of 81. He was survived by his widow, Bess; a daughter, Capella (Mrs. Alpheus Favour); a son, Earl Jr.; and five brothers (Vesto, Elmer, Edward, Claude and John).

His honors included an honorary D.Sc. from the University of Arizona, Tucson, and an honorary LL.D. from Arizona State College (now Northern Arizona University), Flagstaff.