Other than his birth in Wales in 1635, little else is known about Henry Morgan's early years, or about how he found his way to the Caribbean. In Alexandre Exquemelin's The Buccaneers of America, Morgan is portrayed as being born to a poor farmer and sold as an indentured servant in the West Indies. Morgan took exception to this and to Exquemelin calling him a “pirate,” and he sued the book's English publisher for libel, winning £200 sterling. But despite winning his lawsuit, he never gave a more detailed description of his early life, so the question of how he came to the West Indies remains unanswered.

Whether he was an indentured servant, or whether he came across the ocean by working on a ship or serving in the navy, Morgan eventually ended up in Jamaica, which was a British settlement and an important base for the British Royal Navy and the privateers. Morgan spent his first few years in Jamaica taking part in raids on Spanish towns in Central America, and eventually married his first cousin, Elizabeth. In 1663, he led a raid on a Spanish settlement in Nicaragua, which showed him to be an important military leader. Four years later, he was appointed Admiral of the Brethren of the Coast, succeeding Edward Mansfield, who was killed during a raid on Havana, Cuba.