The command reports directly to Navy Medicine East, and itself maintains branch locations at Naval Submarine Base New London in Groton, Connecticut, NSA Saratoga Springs, and in Kittery, Maine.

With the opening of the Naval Training Center in 1883, the spread of disease among the sailors became a significant issue.

[14][15] On September 28, 2016, the City council of Newport, RI voted to re-purpose the waterfront land at the Naval Hospital site as a public park.

In 2009, Captain Elaine C. Wagner assumed command of Naval Health Clinic New England.

[21] In 2010, Captain Marcia Lyons would assume command of Naval Health Clinic New England from Wagner, only to be relieved of duty by her in 2012.

[7] In 2020, Naval Health Clinic New England stopped supporting military families and dependents due to reductions caused by the National Defense Authorization Act (NDAA) 2017.