At 6.22 miles (10.01 km) in length, it connects NY 52 and NY 55 between the hamlets of Stormville (within the town of East Fishkill) at the west end and Poughquag (within the town of Beekman) at the east.

It heads northeast into the center of Stormville and intersects with Old Route 52, a former alignment of NY 52.

[3] In the mid-1920s, NY 39 was assigned to an alignment extending from Poughkeepsie to Patterson via East Fishkill, Stormville and Poughquag.

Route 52 was relocated onto NY 216 between Stormville and Ludingtonville, from where it followed a new roadway south to Lake Carmel.

[7][8][9] The alignment of NY 216 remained unaltered until January 1, 1970, when Route 216 was truncated to its current eastern terminus in Poughquag.