Joeseph, Jr. entered Harvard in 1934 and graduated in 1938. There he played football and rugby and served on the student council. He attended Harvard Law School, but left before his final year to volunteer as a Navy flier. He earned his wings in May 1942 and was sent to England in September 1943. He flew missions throughout the winter of 1943-44
In July 1944, he volunteered for a special mission piloting a modified version of the PB4Y Liberator cargo plane intended to counter the German V-2 rocket attacks on England. The plane was to be loaded with 21,170 lbs of high explosives, flown across the English Channel, where the pilot and co-pilot would parachute out, and then crash into a German V-2 base. The final crash was to be guided remotely by an escort fighter through radio-control. The pilot and co-pilot were to be recovered by ships in the Channel. Before the pilots ejected, the plane was engulfed in a massive explosion. His body was never recovered. He was poshumously awarded the Navy Cross.
In 1946, the US Navy named a destroyer for him, the USS Joseph Kennedy, Jr. DD850. Among the highlights of its service include the blockade of Cuba during the Cuban Missle Crisis and the afloat recovery teams for Gemini-6 and Gemini-7 It is now a floating museum in Battleship Cove, Fall River, Massachusetts.