In the 1930 renumbering, NY 3 was rerouted to exit Watertown to the east on its modern alignment. The former alignment of NY 3 from Watertown to Clayton was then redesignated as NY 12E. By 1935, an alternate route of NY 12E extending from the modern junction of NY 12E and NY 180 to downtown Watertown along the northern bank of the Black River was designated NY 12F. The alignments of NY 12E and NY 12F east of what is now NY 180 were swapped between 1938 and 1942, placing both routes on their current alignments.
On August 1, 1979, maintenance of NY 12E between Broadway in Cape Vincent and the Brownville village line, as well as the portion of Bridge Street in the town of Hounsfield, was transferred from Jefferson County to New York State as part of a larger highway maintenance swap between the two levels of government. In return, the county assumed maintenance of NY 12E between Bridge Street in Brownville and the Watertown city line. Within Brownville, the state also assumed maintenance of NY 12E west of Bridge Street and the remainder of Bridge Street; both had previously been village-maintained. Following the swap, the segment of NY 12E between Bridge Street and the Watertown city limits became concurrent with County Route 190 while Bridge Street became New York State Route 971H, an unsigned reference route.
Current signage along NY 12E indicates that the route has been rerouted east of Bridge Street to follow NY 971H across the Black River to a terminus at NY 12F. However, the 2007 New York State Department of Transportation (NYSDOT) description of routes in New York and the 2006 NYSDOT Traffic Data Report both indicate that NY 12E's southern terminus is still located at NY 12 in downtown Watertown.