His parents, Samuel and Sarah (Soole) Hinckley, were followers of the Nonconformist minister John Lothropp, in whose church at nearby Hawkhurst Thomas was baptized on March 19, 1618.

Hinckley appears to have been comparatively moderate in dealing with the Quakers; while some called for them to be banished, whipped, or even executed (as happened in the neighboring Massachusetts Bay Colony), the law imposed fines for acts such as getting married without the services of an approved minister.

In 1675, Hinckley was called to military service in King Philip's War, serving as the colony's commissary general for the expedition that included the Great Swamp Fight in December 1675.

He was elected deputy governor in 1680, a new position created due to the ill health of then-governor Josiah Winslow, and the great age of John Alden, then the senior assistant.

The dominion collapsed in 1689 after the Glorious Revolution propelled William and Mary to the English throne, and prompted the 1689 Boston revolt, in which Andros was arrested and returned to England.

It was thought that Plymouth, a relatively poor colony, would be absorbed by one of its larger and more economically successful neighbors, either Massachusetts or New York (which then included Martha's Vineyard and the Elizabeth Islands).