Thomas Flucker built a prosperous Boston mercantile business before entering the colony's highest administrative circles. Surviving accounts record transactions from the 1750s onward, including business associated with the Broad Bay settlement in Maine. Through his marriage to Hannah Waldo he was connected with Samuel Waldo's eastern land interests, and his correspondence with Francis Bernard concerned the development and division of township property.

George III commissioned Flucker as secretary of Massachusetts Bay on November 12, 1770, succeeding Andrew Oliver. He took the required oaths in March 1771. The commission authorized him to exercise the office personally or through deputies, with its customary fees and privileges, during the king's pleasure and residence in the province. He also joined the royal mandamus council in 1774, aligning his public position with the Crown as resistance to British authority intensified.

The Revolution divided his household. His daughter Lucy married Boston bookseller Henry Knox in 1774 against the family's wishes and supported the American cause, while Flucker remained a Loyalist. He left Massachusetts and settled in England, where he belonged to the circle of displaced colonial officials and merchants around Brompton Row. He did not return to resume his American business or office. His death in London in 1783 ended a career in which commerce, eastern land development and royal administration had become bound to the political conflict.