On September 24, 1941, Kennedy, with the help of the director of the Office of Naval Intelligence (ONI) and the former naval attaché to Joseph Kennedy, Alan Kirk, joined the United States Naval Reserve. He was commissioned an ensign on October 26, 1941,[38] and joined the staff of the Office of Naval Intelligence in Washington, D.C.[39][40][41]

Lieutenant (junior grade) Kennedy (standing at right) with his PT-109 crew, 1943
In January 1942, Kennedy was assigned to the ONI field office at Headquarters, Sixth Naval District, in Charleston, South Carolina.[40] He attended the Naval Reserve Officer Training School at Northwestern University in Chicago from July 27 to September 27[39] and then voluntarily entered the Motor Torpedo Boat Squadrons Training Center in Melville, Rhode Island.[40][42] On October 10, he was promoted to lieutenant junior grade.[40] In early November, Kennedy was still mourning the death of his close, childhood friend, Marine Corps Second Lieutenant George Houk Mead Jr., who had been killed in action at Guadalcanal that August and awarded the Navy Cross for his bravery. 