In 1669 Burnet became Professor of Divinity at Glasgow University. However, he resigned five years later after a disagreement with his patron, the Duke of Lauderdale. He now moved to London where he became an active supporter of the Whigs.
In 1683 Bumet was accused of plotting against James II and he was forced to flee to Holland. When William of Orange became king he appointed Bumet as his royal chaplain. Later Bumet became Bishop of Salisbury.