It rises in the southeastern part of the town of Berne, west of the Helderberg Mountains, and flows west, passing through the hamlets of East Berne, Bensons Corner, Berne, and West Berne, continuing through the town of Wright, where it passes the hamlets of Gallupville and Shutter Corners before entering the town of Schoharie, where it flows into Schoharie Creek near the hamlet of Vroman Corners.

The United States Geological Survey (USGS) maintains stream gauges along Fox Creek.

The station on Drebitko Road, 2.9 miles (4.7 km) northeast of Schoharie has been recording daily measurements since 2017.

[3] Louse Kill converges with Fox Creek near Schoharie, New York.

[4] Ox Kill converges with Fox Creek near Gallupville, New York.