The hospital was founded by Mother Mary Aikenhead, foundress of the Roman Catholic order Religious Sisters of Charity, on St Stephen's Green, Dublin, in 1834. The hospital was open to all who could afford its services, irrespective of their religious persuasion. The hospital was legally registered as a company on 28 March 1927. The hospital was subsequently moved to its current site in Elm Park in 1970, and in 1999 was renamed St. Vincent's University Hospital, to highlight its position as a principal teaching hospital of University College Dublin. Along with St. Michael's Hospital and St. Vincent's Private Hospital, it is part of the St. Vincent's Healthcare Group (SVHG).

The first kidney transplant in Ireland took place in St. Vincent's Hospital on 19 December 1963.

In May 2013, it was announced that the new National Maternity Hospital, Dublin would relocate to the site of St. Vincent's University Hospital and that the Sisters of Charity were to have responsibility for owning and managing the new hospital. On 29 May 2017, in response to weeks of pressure and public concern, the Sisters of Charity announced that they were ending their role in St Vincent's Healthcare Group and would not be involved in the ownership or management of the new hospital; the two sisters on the board resigned. This was described as "a major turning point in the history of religious involvement in Irish healthcare."

On 8 May 2020 it was announced that the Religious Sisters of Charity would transfer ownership of St Vincent's Healthcare Group to the state. The confirmed that they had received permission from the Holy See to transfer the property, worth some €200 million. The St Vincent's Healthcare Group site could then be transferred from the ownership of the religious order to a new independent charitable group to be called St Vincent's Holdings CLG.