His first command was "PT-101" from December 7, 1942, until February 23, 1943: It was a patrol torpedo (PT) boat used for training while Kennedy was an instructor at Melville. He then led three Huckins PT boats—"PT-98", "PT-99", and "PT-101", which were being relocated from MTBRON 4 in Melville, Rhode Island, back to Jacksonville, Florida, and the new MTBRON 14 (formed February 17, 1943). During the trip south, he was hospitalized briefly in Jacksonville after diving into the cold water to unfoul a propeller. Thereafter, Kennedy was assigned duty in Panama and later in the Pacific theater, where he eventually commanded two more PT boats.