The stream flows north from the source through a housing development and intersects Route 27 nine miles from where the highway crosses the Raritan River in New Brunswick, hence its name.

However, it may be visible as a pipe on the right side of Route 27 in the area across from Stillwell Road when driving south.

From Route 27, the Nine Mile Run meanders through a wooded area and crosses Beekman Road.

Continuing north, the stream encounters another wooded area, part of the land set aside for the Six Mile Run Reservoir Site, and crosses Cortelyous Road under a narrow bridge.

It then joins the Six Mile Run east of South Middlebush Road in Franklin Township 40°28′00″N 74°32′13″W / 40.46667°N 74.53694°W / 40.46667; -74.53694.

Some areas have natural floors composed of rock polished smooth by the stream's abrasive action.