Flinders enlisted in the Royal Navy in 1789 at the age of 15, and Pasley secured for him the position of a lieutenant's servant aboard HMS Alert. 
Flinders also served as a crew member under Pasley's command on HMS Scipio and learn the practical skills of being a sailor before becoming midshipman on the famous 74-gun fighting ship HMS Bellerophon in 1790, serving under William Bligh on a voyage to Tahiti in 1791. 
Flinders fought against the French in the naval battle of the Glorious First of June 1794.

In 1795 Flinders sailed to Australia in H.M.S. Reliance in which George Bass was surgeon. There, he carried out vital coastal survey work. He made two hazardous trips with Bass in small open boats, exploring Botany Bay and George's River on the first, and then, after a brief visit to Norfolk Island, going farther south to Lake Illawarra. He rejoined the Reliance for a voyage to the Cape of Good Hope to bring back livestock.

In 1798 Flinders, now lieutenant, joined the schooner Francis on a visit to the Furneaux Islands and carried out useful hydrographic work. A second visit to Norfolk Island followed, after which, in company with George Bass, he circumnavigated Van Diemen's Land in the sloop Norfolk from 7 October 1798 to 12 January 1799, and thus proved it to be an island. 

 In March 1800 he sailed for England in the Reliance, where reports of his outstanding ability had preceded him. While in England in 1801 he published his Observations on the Coasts of Van Diemen's Land, on Bass's Strait and its Islands, and on Part of the Coasts of New South Wales, but he was chiefly concerned with preparation for an expedition whose results were to place him among the foremost navigators of all time.