Elizabeth Peratrovich died after battling breast cancer, on December 1, 1958, at the age of 47. She is buried at Evergreen Cemetery in Juneau, Alaska, alongside her husband Roy who died in 1989. The eldest son, Roy Jr.—a partner in the engineering firm of Peratrovich, Nottingham and Drage—became a noted civil engineer in Alaska and designed the Brotherhood Bridge in Juneau, which carries the Glacier Highway over the Mendenhall River. Her younger son, Frank, worked as the Area Tribal Operations Officer for the Bureau of Indian Affairs in Juneau.