Charlton was born in London, and became a barrister and member of Lincoln's Inn. He was created serjeant-at-law upon the Restoration. In 1661, he was made Judge of the Council of Wales and the Marches, and was knighted and made Chief Justice of Chester in 1662. He was made a King's Serjeant in 1668. Elected to the House of Commons for Ludlow in 1660, he briefly served as Speaker in 1673, pleading ill-health to retire. He left Parliament in 1679, and was forced out of the post of Chief Justice of Chester in 1680 when Judge Jeffreys desired it, being placed in the Court of Common Pleas instead.
Charlton received a baronetcy in 1686, and recovered the Chief Justiceship of Chester, which he left in 1689.