Kernan entered the United States Navy in 1969 and served as a Naval Flight Officer aboard the U.S.S. Kitty Hawk. In May of 1972, Kernan was shot down by the enemy while on a reconnaissance mission over North Vietnam. He was held as a prisoner of war. Kernan was repatriated in 1973 and continued on active duty with the Navy until December of 1974. Kernan received the Navy Commendation Medal, two Purple Hearts and the Distinguished Flying Cross. In 1974 he was married to his wife, Maggie.
Joe Kernan was elected mayor of South Bend in 1987, 1991, and 1995. In 1996, Joe Kernan was elected as Indiana's Lieutenant Governor, and then re-elected in 2000. As lieutenant governor of Indiana, Kernan served as the president of the Indiana Senate, the director of the Indiana Department of Commerce, and as the commissioner of Agriculture.