John Thompson was the only child of David and Amias Thomson to survive childbirth. He was born in Plymouth, England around the beginning of 1619. He likely first came to New England in the Spring of 1623 with his father and mother aboard the ship Jonathan, as part of the Council for New England's project to establish a trading settlement in what is now New Hampshire, of which his father was the leader.

While not much is known of his childhood into early adulthood, he appears to have returned to England for some period of time, and pursued a career as a merchant shipper that saw him rise to the rank of Captain. Circumstantial evidence and known financial problems suggest he may not have been very successful in that line of work.

In the late-1640s he appears in Boston court proceedings defending his ownership of Thompson's Island (granted to his father, as part of David Thomson's 1622 Indenture) from an attempted takeover by the community of Dorchester, and shortly thereafter forteiting the island to English creditors after failure to meet a debt repayment order.

By the early-1650s he is found living in Weymouth, Massachusetts with a family, presumably pursuing a land-based occupation.

In the mid-1660s he, along with about a dozen other men, purchased land west of Medfield, Massachusetts from the Nipmuc Indians and founded the town of Mendon. In 1675 Mendon was burned to the ground and multiple residents were killed in the violence between the native and colonial populations known as King Philip's War, driving the townspeople back to Braintree and Weymouth to the East. (The Thompson family is believed to have resettled in Braintree, given the known birthplace of several of John, Jr.'s children during this time.) When Mendon was rebuilt in 1680, John Thompson and family were some of the first to return to the area, where he remained until his death in 1685. It is assumed he is buried in one of the old town cemeteries under one of the many unidentifiable headstones that can be found there.