Before European settlers arrived, Kingston was within the tribal homeland of the Wampanoag people. Several years before the Mayflower had landed in Plymouth, during the Native American epidemic of 1616 to 1619, the Wampanoag population was severely damaged from a rapidly spreading pandemics due to earlier contacts with Europeans. Several ancient Native American burial sites have been located within the borders of Kingston.
Originally part of Plymouth, Kingston was first settled by Europeans shortly after the landing of the Pilgrims at Plymouth Rock in 1620. It was settled once more in 1635. During 1675, several bloody battles during King Philip's War are believed to have occurred within Kingston's borders and the residence of Governor Bradford, which is now part of Kingston, was raided by Wampanoag warriors.
In 1685, the area was placed within the boundaries of Plymouth County and for a brief time, between 1686 and 1689, the borders of Kingston were within the Dominion of New England.
Kingston was first established as Plymouth's northern precinct in 1717 upon the creation of First Parish Kingston, now a Unitarian Universalist church in the town's center. Kingston was incorporated as a distinct town on June 16, 1726, following a tax dispute between the residents of north and south Plymouth, when the parish was known as the upper class portion of Plymouth. Kingston's borders were carved out of neighboring towns Plymouth, Duxbury, Plympton and Pembroke, all of which were incorporated before Kingston.
Kingston is home to the longest continuously run boat yard in North America, now named the Jones River Landing. The American Revolutionary War era brig, USS Independence, was built by Kingston shipbuilders on the Jones River and has emerged as a town icon, featured on the Kingston town seal, as well as the subject of the town's song, "Independence."
On April 14, 1857, Kingston annexed a small part of Duxbury. It would be the last addition to the town's borders to date.
In the 1950s Kingston was transformed from a small rural town into an extension of the Boston metropolitan area when Massachusetts Route 3 was constructed, connecting Boston to Cape Cod, with two exits in Kingston (and a third exit immediately over the town line in Duxbury).
Kingston saw its largest population growth in the 1990s when the Old Colony Railroad was reopened as a commuter rail line, connecting once-rural Kingston with Boston, making Kingston an even more viable place for commuters to live. More recently, Kingston has seen the construction of four industrial-sized wind turbines, located along Route 3.