He was the son of William Rainsborough, a captain and Vice-Admiral in the Royal Navy, and Ambassador to Morocco (for his services to end white slavery he was offered a baronetcy, which he declined). Before the war, Thomas and his brother, William Rainsborowe, were both involved in an expedition to the Puritan Providence Island colony, off the coast of Nicaragua. Rainsborough commanded the Swallow and other English naval vessels in the first civil war. By May 1645, he was a colonel in the New Model Army, taking an active part in the battles at Naseby and at Bristol. Later that year, he captured the symbolic stronghold of Berkeley Castle. In 1646, he helped conclude the Siege of Worcester.