"John A. Bole" entered San Francisco Naval Shipyard in late 1961 to undergo a major Fleet-Rehabilitation-and-Modernization overhaul, designed to equip her with the latest equipment and lengthen her active service life several years. Emerging in July 1962, she took part in training operations for the remainder of the year, interrupted by several weeks of alert at sea during the Cuban Missile Crisis in October. During the first few months of 1963, she operated out of San Diego, sailing 1 April 1963 for Pearl Harbor and the Western Pacific. This cruise helped to maintain the vital American presence in the Far East, and she returned to San Diego on 3 December 1963. In the first half of 1964, she was engaged in antisubmarine operations, including tests of her new DASH. "John A. Bole" sailed 23 October 1964 for the Western Pacific with a group composed of and other destroyers. After maneuvers in Hawaiian waters, she reported to Commander 7th Fleet on 2 January 1965 to resume peacekeeping operations in the troubled region. During the deployment, the destroyer operated with a carrier task group and an ASW hunter-killer group, then patrolled Taiwan Straits. From 9–25 February, she operated off Vietnam.