Wheeling Hospital, called the mother hospital of West Virginia because of its early founding, was chartered March 12, 1850. It was the only such medical facility between Pittsburgh and Cincinnati, and growth was swift. Its founders were the Catholic Bishop Richard Whelan and Dr. Simon Hullihen, supported by Drs. John Frissell and Matthew Houston. In 1853, the bishop brought in six Sisters of Saint Joseph from Missouri and purchased the Metcalf property, a house still standing at 110 15th Street. In 1856, the hospital outgrew this building and moved to the Michael Sweeney mansion in North Wheeling, its site for the next 119 years.

During the Civil War, in April 1864, a wing of the hospital was rented by the U.S. Army, and in July the entire institution was taken over as a general military hospital. The Sisters were hired as army nurses, treating wounded Union and Confederate soldiers side by side. The institution grew to 90 beds in 1892, and, with two new wings, to 225 beds in 1914. A nursing school was founded in 1900 and discontinued in 1975. Also designated a marine facility, the hospital served the boatmen on the Ohio River for many years.

The original hospital building was demolished and a new central portion constructed in 1933. During World War II, the institution sponsored a Cadet Nurses Corps unit and furnished doctors and nurses for the war effort. After the war, two new departments were opened: physical therapy in 1948 and outpatient in 1950. Wheeling Hospital set up the state's first intensive care unit in 1963 and the first coronary care unit in 1966.

The hospital moved from North Wheeling to a new facility in 1975 at its present location in the Clator neighborhood of Wheeling. In 1978, the region's first cardiac catheterization laboratory was opened, and a second was added in 1996. This made possible the area's first open-heart surgery in 1994. A continuous care and kidney dialysis center was dedicated in 1983. In 1994, the Howard Long Wellness Center opened, increasing innovative programs in cardiac and pulmonary disease rehabilitation. In 2010, the hospital had 276 beds, and 230 primary-care and specialty physicians. Its multi-care facilities include Bishop Joseph H. Hodges Continuous Care Center, the Wheeling Renal Care, the Howard Long Wellness Center and four medical office buildings. Belmont Community Hospital, The Belmont Health Center, St, Clairsville Health Center and Powhatan Health Center (all in Ohio) and Wellsburg Clinic in Brooke County are affiliates of Wheeling Hospital.

In 2017 the hospital was rocked by a whistleblower lawsuit against R&V Associates Ltd., the company that had managed the hospital since 2007. In September 2020 the lawsuit was settled, and Wheeling Hospital became a member of West Virginia University Health Services through a 50 year lease. The hospital maintains its affiliation with the Catholic church.