In 1906,  the Raleigh and Pamlico Sound Railroad Company decided to bring the railroad through the Whitley and Horton family farms in eastern Wake County. Edgar B. Barbee and Falconer B. Arendell organized the Zebulon Company for development that same year.

The company received its charter on February 15, 1906. Shortly thereafter, they began to divide up their 49 acres (20 ha) into lots, blocks, streets and avenues. On February 16, 1907, the town was officially recognized as Zebulon, North Carolina. The town was named after Zebulon Baird Vance, the Governor of North Carolina during the American Civil War. The first election was held in May 1907, and the first elected mayor was Thomas J. Horton.

There are three properties in Zebulon listed on the National Register of Historic Places: Wakelon School, Bennett Bunn Plantation, and the George and Neva Barbee House.