Founded in 1630 at the time of the settlement of Boston, King's Chapel is Boston Proper's oldest burying place. Like the majority of Boston's burying grounds, it has always been under municipal control, not affiliated with any church. The site is said to be part of Isaac Johnson's estate, an esteemed early settler. In 1668 Royal Governor Andros seized a portion of this property to construct the town's first Anglican church, King's Chapel, which was built in 1688.

The earliest graves and tombs were scattered randomly throughout the grounds, with no formal pathways. In the early nineteenth century, landscaped cemeteries outside cities became the public parks of their times and efforts were taken to beautify urban burying grounds. Pedestrian footpaths, an ornamental cast iron fence and various plantings were all installed to enhance visitors' experience in King's Chapel Burying Grounds. Efforts went so far as to rearrange the gravestones in straight rows, frequently not corresponding to the body buried underneath.

Tradition holds that the first interment in King's Chapel Burying Ground was that of the former owner of the property, Isaac Johnson, in 1630. Notables buried here include Massachusetts' first governor, John Winthrop; William Dawes, Paul Revere's compatriot on his ride to Lexington in 1775; the Reverend John Cotton, a powerful religious leader in seventeenth-century Boston; Hezekiah Usher, the colonies' first printer and publisher; and Mary Chilton, who many believe was the first woman to step off the Mayflower.

The Massachusetts Historical Commission refers to this cemetery in MACRIS as BOS.803 King's Chapel Burying Ground.