John Paul Jones, second of the initial class destroyers of post-war design, conducted exhaustive shakedown training out of Guantanamo Bay, Cuba, after which she departed for a cruise to Northern Europe and the British Isles.

During this voyage Commander Hayler and members of the crew visited the birthplace of John Paul and presented the ship's emblem to the people of Kirkcudbright.

In April 1962 she took part in a fleet review and weapons demonstration for President John F. Kennedy, and in July she again embarked midshipmen for training.

In October 1962 the ship was on station with the Atlantic Recovery Forces during the orbital flight of Commander Wally Schirra, and soon afterward moved off the coast of Cuba during the Cuban Missile Crisis.

John Paul Jones headed back to the Mediterranean 18 June for NATO exercises with units of the French, Greek and British navies.

John Paul Jones was converted to a guided missile destroyer at the Philadelphia Naval Shipyard between 20 December 1965 and 15 March 1967 and designated DDG-32.