The Hillsboro Inlet (as well as the town of Hillsboro Beach) was named by surveyor William DeBrahm in the 1770s.

The French and Indian War awakened the British government to the need for better maps of its North American empire, and with the advent of peace, a program was established for mapping the entire Eastern seaboard. To accomplish this, the colonies were divided north and south at the Potomac River and a surveyor general appointed for each district--William DeBrahm for the Southern District. . . . As instructed, DeBrahm concentrated his efforts on the Florida peninsula south of St. Augustine. His were the first scientific surveys of the peninsula, which heretofore appeared on most maps of the area as a collection of narrow islands, and he produced the first printed map of the Gulf Stream.

"Hillsborough Outlet" was the name given the inlet by DeBrahms; it is not clear how the spelling changed. The Hillsboro in question was Lord Wills Hill, Earl of Hillsborough. He was Secretary of State for the Colonies from 1768 to 1772, and a fierce opponent of allowing any concessions to the American colonists. He was also described by a contemporary as "a pompous composition of ignorance and want of judgment."