Charles Hotham (1615, Scorborough – ca. 1672, Bermudas) was an English cleric.
Charles Hotham was the son of Sir John Hotham, Governor of Hull. He was educated at Westminster School and Christ's College, Cambridge, where he gained his MA in 1639. He became a fellow of Peterhouse, Cambridge in 1640, but was deprived by parliament of his fellowship in 1661. He became vicar of Withernsea, Yorkshire from 1640 to 1644 and rector of Wigan from 1653 until ejected for unorthodoxy in 1662, at which point he went as a minister to the Bermudas. He became a Fellow of the Royal Society in 1667 and died in the Bermudas in 1672.
Hotham wrote Ad philosophiam Teutonicam Manuductio in 1648, and translated Jakob Boehme's Consolatory Treatise of the Four Complexions in 1664.
He married on 15 September 1656 Elizabeth, daughter of Stephen Thompson of Humbleton, Yorkshire. Their son Charles became Sir Charles Hotham, 5th Baronet and MP for Beverley.