The area was named by Benjamin Ware, a hotelier who developed Clifton with the intention of creating a resort area. His hotel, "Clifton House", was regaled as one of the finest lodgings in the county. In 1884, Ware attempted to subjugate all of Marblehead Neck, and the southeastern coastline of the town, along with his resort community, and form the Town of Clifton Village. The Committee on Towns eventually denied his proposal.
A branch of the Portland division of the Boston & Maine Railroad had a station in Clifton in the 1920s. The railway is gone and the site of the station can still be seen from Clifton Avenue. The track bed is now a bike path that extends from neighboring Swampscott in the south to Salem in the north.
Attractions in the area included the Clifton House and the Tedesco Country Club, which is still fully operational.
In current times, Clifton encompasses the whole of the southeastern ocean front of Marblehead and incorporates the areas known as Greystone, Clifton Heights (Peabody Camp), Clifton and Rockaway. There are a number of associations that serve to preserve and improve these neighborhoods: Clifton Improvement Association and Clifton Heights Improvement Association are of particular note for the work they have done.