Commander Navy Region Europe Command traces its roots back to a hand shake between Winston Churchill and General Dwight D. Eisenhower in 1941. In 1942 Admiral Harold F. Stark set up offices at 20 Grosvenor Square (7 North Audley Street), marking the beginning of the leadership of U.S. Naval Forces Europe (CNE).
In November 2001, as part of a realignment effort undertaken by CNE, Rear Adm. David T. Hart Jr., as CNE Deputy, took on the additional duty as Navy Region Europe's (CNRE) commander. Three years later, Commander Maritime Air Allied Naval Forces South (COMMARAIRSOUTH) was renamed Commander Maritime Air Naples (CMAN) under CNRE’s cognizance. It was at this time that CNRE started relocating from London to Naples, Italy, relinquishing the lease on the Navy building rented from the Duke of Westminister for 100 pounds per year.
In January 2009, operational and logistical shore service support of Navy Region Southwest Asia, along with Camp Lemonnier, Djibouti, was realigned under the scope of Navy Region Europe. On April 21, 2009, Navy Region Europe officially changed its name to Commander Navy Region Europe, Africa, Southwest Asia.