In 1632 Middle Plantation was established as a fortress in the ongoing conflicts with Native Americans. It became the site of the College of William and Mary in 1693 and became the location of the capital in 1699 after Jamestown was burned (again) in 1698. Shortly thereafter, Middle Plantation was renamed Williamsburg in honor of King William III of England. The capital was moved to Richmond in 1780 at the outset of the American Revolution. The Battle of Green Spring was fought in the county just a short time before the British surrender at Yorktown. (Green Spring Plantation was the former home of Royal Governor William Berkeley).

During the American Civil War, the Battle of Williamsburg was waged in York and James City County during the Peninsula Campaign in 1862. After the War, Collis P. Huntington extended the new Chesapeake and Ohio Railway through the county to reach new coal piers he had built at at Newport News on Hampton Roads. Railroad stations were established at Diascund, Toano, Norge, Kelton, Williamsburg, and Grove. In Williamsburg, the temporary tracks initially laid ran down the middle of Duke of Gloucester Street.

Williamsburg became an independent city from the county in 1884, after a change in the Virginia constitution in 1871. Williamsburg and James City County share a combined school system, courts, and some constitutional officers. Beginning in the early 20th century, preservation and restoration efforts resulted in a major increase in tourism to the county and surrounding area. Attractions developed included Colonial Williamsburg, Jamestown Settlement, the Colonial Parkway, Carter's Grove Plantation, and Busch Gardens. At the turn of the 21st century, new archaeological work was underway at Jamestown and nearby Green Spring Plantation, with the promise of new historical discoveries.