He was of Huntingdonshire parentage and educated at Westminster School and Jesus College, Cambridge. He had become interested in antiquarian studies under William Camden, and began to amass a library. He entered Parliament as a member for Huntingdon in 1601. He helped devise the institution of the title baronet as a means for King James I of England to raise funds. Despite his early period of goodwill with James I, during which he was made a baronet, Cotton's politics became anti-royalist in nature and the authorities began to fear the uses of his library, which was confiscated in 1630 and returned only after his death to his heirs.