Its eastern terminus is at a junction with U.S. Route 11 (US 11) in the hamlet of Messengerville within the Cortland County town of Virgil.

It continues northeast, intersecting CR 128 (Owego Hill Road) before entering the hamlet of Virgil.

Past Virgil, it continues on an easterly routing for 2 miles (3.2 km) before curving to the southeast.

[5] This section of NY 90 remained unchanged for the next half-century,[2] save for an April 1, 1981, highway maintenance swap that transferred ownership and maintenance of the Virgil–Messengerville segment's easternmost mile from Cortland County to the state of New York.

[6] On April 1, 1980, ownership and maintenance of East Main Street and Virgil Road from NY 13 and NY 38 in the village of Dryden to the Tompkins–Cortland county line was transferred from Tompkins County to the state of New York as part of a highway maintenance swap between the two levels of government.