NC 99 was born in the early-1930s, being routed over a previously unnumbered road in Beaufort County. The road ran north from US 264 to a modern-day secondary road (which, at that time, was the first incarnation of NC 97).
Around the late-1930s, the highway's current alignment began to take shape. The original 99 was reassigned as an extension of NC 32, and NC 99 was given its current assignment as a state highway through Washington County and Beaufort County. The southern terminus was originally at US 264 in Pantego, North Carolina.