In November 1989, Kinkaid and the Panamanian-registered freighter M/V Kota Petani were involved in a collision in the Strait of Malacca. The collision caused one death and 15 other casualties to the Kinkaid's crew, and US$15 million in damages to Kinkaid. She made Singapore under her own power for temporary repairs, then Subic Bay, Philippines, then San Diego, California for permanent repairs.
On 4 July 1993, Kinkaid paid a three-day port visit to Acajutla, marking the first visit by a U.S. warship to El Salvador in more than a dozen years. Kinkaid was then assigned to Destroyer Squadron 13 in San Diego and was, at the time, conducting two months of routine operations under the operational command of Joint Task Force Four, located in Key West, Florida. Kinkaid returned to San Diego in mid-August.
Kinkaid deployed on 10 November 1994, as part of the carrier battle group for a six-month deployment to the western Pacific, Indian Ocean and Persian Gulf. She spent most of December in the Western Pacific. With the Constellation carrier battle group, she entered the Persian Gulf, on 11 January 1995, and departed it on 23 March. The Constellation carrier battle group conducted several exercises during the deployment, including Beachcrest 95, a routine annual exercise that included air combat, air control and air-to-ground combat support training in designated areas on Okinawa and Ie Shima; Nautical Swimmer 95-2 and Nautical Artist 95-2, naval air and surface exercises intended to improve interoperability between forces of the U.S. and friendly Persian Gulf nations; Beacon Flash 95-1, a combined naval tactical air exercise to improve readiness with friendly Persian Gulf nations; Eager Archer 95-1, an air training exercise between units of CVW 2 and Kuwait that provided dissimilar air combat training, formal joint strike training and in-flight refueling training for the Kuwaiti air force; and Sharem 110, a U.S. anti-submarine warfare (ASW) training exercise in the Gulf of Oman involving several battle group units. The battle group also conducted exercises with units of the Royal Australian Navy off the coast of western Australia. Kinkaid made its seventh deployment and supported the battle group by performing the anti-submarine warfare mission.
Kinkaid underwent a period of overhaul in June 1995. As a result of a reorganization of the Pacific Fleet's surface ships into six core battle groups and eight destroyer squadrons, Kinkaid was reassigned to Destroyer Squadron 21. The reorganization was scheduled to have been completed by 1 October 1995, with homeport changes to be completed within the next year.
In mid-1997, as part of the carrier battle group, Kinkaid took part in Pacific Joint Task Force Exercise 97-2 (JTFEX 97-2). The exercise was conducted off the coast of southern California and also included units from the Air Force, Army and Japan. Nimitz, from 20 July through 24 July, then conducted a warfighting demonstration called Surge Exercise (SURGEX), during which it demonstrated the firepower of the carrier/airwing team and its ability to sustain continuous operations in support of forces ashore in the initial four days of a conflict when a deployed carrier might be the only asset available to provide such support. During the exercise, , Kinkaid and practiced maritime interception operations. Kinkaid also escorted the civilian merchant ship Viking Serenade through the simulated "war zone".
Kinkaid then deployed as part of the Nimitz carrier battle group. After Western Pacific visits in Yokosuka, Japan, and Hong Kong, a planned visit to Singapore was canceled when Iraq violated a United Nations imposed "no fly" zone. With Nimitz directed to proceed to the region immediately to reinforce Operation Southern Watch operations, Kinkaid arrived in the Persian Gulf on October 12 after transiting the Strait of Hormuz.
During Nimitz's deployment in the Persian Gulf, Kinkaid was accused by Iran of spying on its military exercises. Kinkaid was, however, in port in Bahrain at the purported time Iran claimed the spying was taking place.
Kinkaid returned on 28 February 1998, from a six month Persian Gulf deployment. During the deployment Kinkaid served as Tomahawk ready strike platform, helped enforce the no-fly zone in Southern Iraq and conducted maritime interception operations.
Kinkaid was part of the Constellation carrier battle group, as the Constellation officially relieved in the Persian Gulf in September 1999. The Constellation carrier battle group then spent the next 10 weeks in the Persian Gulf and conducted maritime interception operation boardings as well as flew combat air patrols over the Iraqi no-fly zones in support of Operation Southern Watch. During the period, Kinkaid rescued the M/V Sima Star, a container ship, from sinking 70 miles (130 km) off the coast of Bahrain after taking on over 40 tons of water. Kinkaid sailors dewatered the fully loaded container ship, which was listing 15 degrees to the port side. After seven hours of battling poor ventilation and flooding below decks, Kinkaid's rescue and assistance team was able to return the Sima Star to a five degree list, allowing its crew to sail into Bahrain the following Monday morning for repairs. Kinkaid returned home on 17 December 1999, after a six-months deployment. During its 10-week patrol in the Persian Gulf region, the Constellation carrier battle group flew more than 5,000 casualty-free sorties, including nearly 1,300 in support of Operation Southern Watch. These flights included nine separate combat strikes and more than 43 tons of ordnance expended on various Iraqi air defense sites in response to Iraqi aggression against coalition aircraft.
Kinkaid began, on 15 March 2001, a scheduled six-month 2001 Western Pacific (WestPac) deployment while attached to the Constellation carrier battle group (CVBG) and Amphibious Ready Group (ARG). The entire battle group had trained the previous six months in preparation for this deployment through a series of increasingly challenging exercises and operations. These pre-deployment exercises culminated in February 2001 with the successful completion of Joint Task Force Exercise 01-1. Over the following six months, battle group ships conducted multi-national and joint operations with the navies of various allied countries and visit ports in Western Pacific and Persian Gulf nations. The ships and squadrons were scheduled to return home in September.
The U.S. Navy Surface Force was scheduled to begin, in the summer of 2002, an initiative to test the effectiveness of deploying a single ship for 18-months while swapping out crews at six-month intervals. Called Sea Swap, this initial two-phased initiative would involve three Spruance-class destroyers (DDs)—, Kinkaid and , and three Arleigh Burke-class destroyers (DDGs)—, , and . For the DD phase, Fletcher and her crew would deploy with their battle group this summer, but after six months, only the crew would return. The ship would remain deployed and be manned by the crew from Kinkaid. After completing their training cycle and decommissioning Kinkaid, these sailors would fly to a port in either Australia or Singapore to assume ownership of Fletcher and steam her back on-station. After six months, they would be replaced by the crew from Oldendorf who would have completed the same training and decommissioning schedule with their ship before flying out to relieve the Kinkaid crew. After four more months on station, the Oldendorf crew would then bring Fletcher back to the United States where it too would be decommissioned. Additionally, by executing this plan, the Navy would be able to eliminate the deployment of because the additional on-station time generated by swapping out the crews meant a ship would already be in theater meeting that requirement.