Hawkins was apprenticed as a clerk and became a solicitor. In 1759 a legacy enabled him to sell his practice. A Middlesex magistrate from 1761, Hawkins was elected chairman of the quarter sessions in 1765. He was knighted in 1772.

Hawkins wrote, among other works, an annotated edition of Izaak Walton's Compleat Angler (1760) and legal articles. His biography of Samuel Johnson (Johnson, Samuel), published with his 1787 edition of Johnson's works, was superseded only by Boswell's. Hawkins was among Johnson's closest friends and was an executor of Johnson's will.

Hawkins' General History of the Science and Practice of Music occupied him for 16 years. It was published in five volumes in 1776, a few weeks before Charles Burney's celebrated General History of Music. Hawkin's book continues to be invaluable as a mine of detailed information, some of it unavailable elsewhere, but it was eclipsed by Burney's.

A kinsman of Sir Francis Drake, Hawkins began his career as a merchant in the African trade and soon became the first English slave trader. By carrying slaves from Guinea, in West Africa, to the Spanish West Indies, he provoked conflict with the Spaniards, who did not allow unauthorized foreigners to trade with their colonies. Hawkins' first slave-trading voyage, in 1562–63, on behalf of a syndicate of London merchants, was so profitable that a more prestigious group, including Queen Elizabeth I, provided the money for a second expedition (1564–65). His third voyage, with Drake (Drake, Sir Francis) in 1567–69, however, ended in disaster. After selling the slaves in the Caribbean, Hawkins was forced by needed repairs and lack of water to take refuge at San Juan de Ulua, near Veracruz, Mex. A Spanish fleet attacked him in the harbour, and, of the six ships, only the two commanded by Hawkins and Drake were able to escape. This episode marked the beginning of the long quarrel between England and Spain that eventually led to open war in 1585.

Hawkins soon avenged himself; by gaining the confidence of Spain's ambassador to England, he learned the details of a conspiracy (the so-called Ridolfi plot of 1571 (Ridolfi, Roberto)) in which English Roman Catholics, with Spanish assistance, were to depose Queen Elizabeth and install Mary Stuart, Queen of Scots, on the English throne. Hawkins notified his government, and the English plotters involved were arrested.

In 1577 Hawkins succeeded his father-in-law, Benjamin Gonson, as treasurer of the navy; later (1589) he was to assume the additional duties of controller. His high naval post enabled him to direct the rebuilding of the older galleons and to contribute to the design of faster, more heavily armed ships. It was this new, swift-sailing navy that withstood the Spanish Armada in 1588. Hawkins was third in command during the Armada crisis (during which he was knighted), and afterward he devised the strategy—quite original for that period—of setting up a naval blockade at the Azores to intercept Spanish treasure ships returning from the New World.

In 1595 Hawkins and Drake sailed with 27 ships to raid the Spanish West Indies. Hawkins died the night before an unsuccessful attack on Puerto Rico.