The provision of healthcare was established at the time Naval Air Station, Whidbey Island was commissioned in 1942. Originally a department under the Naval Air Station and funded by the Bureau of Weapons and Docks, the hospital was located in the building that now houses Skagit Valley College, just outside the main gate to the Seaplane Base. The Family Practice Clinic, consisting of Pediatrics, Medical Clinic, Aviation Medicine, and Dental, was in building 243 located on Ault Field where the Navy Legal Services Office is now. The hospital at the Seaplane Base had Surgical and Outpatients Clinics, OB/GYN, Operating and Delivery Rooms, Pharmacy, Laboratory, Supply, and administrative offices.

On 1 July 1968, the Medical Department of Naval Air Station, Whidbey Island, became Naval Hospital Whidbey Island. The military population growth in the area required an expanded facility, and the move to the present Ault Field building was accomplished in September 1969. Over the years, temporary spaces for Family Practice, Social Work, Supply, and some administrative functions and small departments caused the Naval Hospital to evolve into a complex of buildings.

The command became Naval Hospital Oak Harbor on 1 October 1983. Shortly thereafter, the Naval Hospital sought and received its first accreditation by what is now the Joint Commission. The three-year projects of addition and renovation to the original Ault Field hospital were completed in 1989-1990 timeframe. The current facility has a 12-bed capability and totals over 108,000 square feet of inpatient and outpatient space.

In 1992, two modular buildings were added to accommodate the Occupational Health, Industrial Hygiene, Preventative Medicine, and Mental Health Departments, and a new Aviation Physiology building was dedicated.

One other modular building was added in 1996, to house the Staff Education Training Department and Health promotions. In September 2003, a 781 square foot addition was completed to house the Computed Tomography (CT) scanner. In 2009, a 2,500 SF modular building was added to accommodate the Automated Neurocognitive Assessment Metrics (ANAM) to meet new mission requirements.