The route entered East Fishkill, where it began to turn northeastward through Stormville and the hamlet of Green Haven.

It then passed just south of Beekman, where it started to once again turn southeastward.

NY 39 passed through Poughquag and Pawling, and subsequently ran along the western shore of Whaley Lake.

From here, the route entered Holmes prior to passing into Putnam County.

[2][3][5] In the 1930 renumbering of state highways in New York, the portion of NY 39 between East Fishkill and the western fringe of Patterson was redesignated as part of the new NY 52 while the segment between Poughkeepsie and East Fishkill was renumbered to NY 202.