All of NY 96, except from Candor to Ithaca and from northwest of Victor to Pittsford, was originally designated as part of New York State Route 15 in 1924. NY 15 was originally routed on modern NY 96B between Candor and Ithaca, and modern NY 64 and NY 251 between Victor and Pittsford. It was realigned onto the modern alignment of NY 96 between Victor and Pittsford in 1930. NY 15 was renumbered to New York State Route 2 to eliminate duplication with U.S. Route 15 (US 15). NY 2 was subsequently redesignated as NY 96 in 1942 as the alignments of NY 2 and NY 96, a route in Rensselaer County, were swapped. NY 96 was realigned again in the early 1950s, this time between Candor and Ithaca, to serve the village of Spencer west of Candor. Near Rochester, NY 96 followed what is now Interstate 490 (I-490) for a short time during the 1950s and early 1960s. The 2017 route log erroneously shows that NY 96's northern terminus ends at Union Street.