Gilbert was the fifth son of Otho Gilbert of Compton, Greenway and Galmpton, all in Devon, by his wife Catherine Champernowne. His brothers Sir John Gilbert and Adrian Gilbert, and his half-brothers Carew Raleigh and Sir Walter Raleigh, were also prominent during the reigns of Queen Elizabeth I and King James I. Catherine Champernowne was a niece of Kat Ashley, Elizabeth's governess, who introduced her young kinsmen to the court. Gilbert's uncle, Sir Arthur Champernowne, involved him in the plantation of Ireland between 1566 and 1572.