In Dunkirk, NY 39 originally began at the intersection of East Lake Shore Drive (NY 5) and Main Street. From there, it followed Main Street, Franklin Avenue, and Roberts Road to US 20. NY 39 was truncated to its current western terminus east of the city in the mid-1960s; however, the portion of its former routing outside of the Dunkirk city limits remained state maintained as an unsigned reference route, NY 837. On April 1, 1980, ownership and maintenance of it was transferred from the state of New York to Chautauqua County as part of a highway maintenance swap between the two levels of government. The Roberts Road segment of NY 39's former alignment is now part of CR 81 while the Main Street portion is now the northernmost part of NY 60.