The southern terminus of the route is at an interchange with NY 17 (Future Interstate 86) in the town of Sanford in Broome County, New York.

The route is almost 100 miles (161 km) long and passes through Broome, Chenango, Cortland, and Onondaga counties.

The route initially extended as far north as Jordan; however, NY 41 was cut back to its current northern terminus c. 1933.

The route heads north, following Oquaga and Cornell Creeks through a series of valleys in the rural eastern portion of Broome County.

Now in the town of Afton, NY 41 passes under Interstate 88 (I-88) just south of an intersection with County Route 26 (CR 26).

NY 41 turns northwest at this junction, following Maple Avenue across the Susquehanna River and into the center of the village.

[3] The two routes converge here and head west to the hamlet of Coventry, where they intersect the northern end of NY 235.

NY 41 heads northwest from this junction, passing by Long Pond and Cincinnatus Lake before crossing into Cortland County and the town of Willet.

All three routes turn north here, following Church Street for three blocks to Clinton Avenue.

[3] Here, maintenance of the route shifts from the New York State Department of Transportation (NYSDOT) to the city of Cortland.

This new route was, at the time, designated from McClure (beginning at an intersection with NY 17) through Afton and Greene to Cortland, where it met US 11.