The highway extends 54.32 miles (87.42 km) from Main Street (U.S. Route 9 or US 9) in Tuckerton to CR 535 in Cranbury Township.

Much of the two-lane route passes through isolated areas of the Pine Barrens and the eastern end of the Fort Dix entity of Joint Base McGuire–Dix–Lakehurst.

Upon crossing into Stafford Township, the road passes through the small residential community of Warren Grove, where it intersects CR 608.

Following this junction, the route enters more wooded areas of residential development, passing New Egypt Speedway before crossing CR 528.

The route heads through more areas of farms, woods, and residences, where it turns west onto Davis-Allentown Road at a roundabout with CR 539 Alt.

The road leaves Allentown for Upper Freehold Township and enters farmland as it intersects CR 526 Spur.

CR 539 continues northeast past a mix of farms and residential subdivisions before passing through more agricultural surroundings.

The road briefly turns east and runs through a wooded part of Millstone Township, Monmouth County.

The road heads back into East Windsor Township and runs through farmland, passing under Route 133.

The road passes near housing developments, becoming South Main Street as it crosses the Millstone River into Cranbury Township, Middlesex County, in wooded areas.

[3] A Monmouth County-takeover of Sharon Station Road in Upper Freehold known as County Route 539 Alternate occurred in 2009.

or CR 539A) is a 1.47-mile-long (2.37 km) Monmouth County-maintained segment of Sharon Station Road in Upper Freehold Township.

Its entire length is a divided highway with one lane in each direction and jughandles for U-turn movements and a northbound entrance to Dutchess Drive.

It travels north through farmland over Doctors Creek before passing to the east of housing developments.