The original highway was decommissioned by 1940 but was reestablished running from US 264 in Pantego to NC 32 south of Plymouth.

From its southern terminus, NC 99 begins by heading to the east, running adjacent to the Pamlico River.

Following the crossing of a tributary of the Pamlico River, it makes several turns and begins running east.

It runs to the northeast in Belhaven, crossing a railroad operated by the Carolina Coastal Railway.

[1][3] Travelling north of Belhaven, US 264 and NC 99 generally parallel the Carolina Coastal Railway line.

US 264 and NC 99 enter Pantego from the west, picking up the name Main Street and initially traveling through a residential area.

For 0.4 miles (0.64 km), NC 99 is routed to the northwest, largely paralleling the Pungo River.

It makes several curves that give NC 99 a northerly orientation, and the highway begins to parallel a canal.

[1][3] The North Carolina Department of Transportation (NCDOT) measures average daily traffic volumes along many of the roadways it maintains.

In 2016, average daily traffic volumes along NC 99 varied from 1,100 vehicles per day southwest of the intersection with Sidney Road in Beaufort County to 5,400 vehicles per day southwest of the intersection with US 264 and US 264 Business in Belhaven.