He was elected Governor of Vermont in 1813, replacing his brother-in-law, Jonas Galusha, who was also his successor in the post. Chittenden served as governor from October 23, 1813 until October 14, 1815. He was the last Federalist governor of Vermont. During his term as governor, fighting between American and British forces was fierce on the current United States–Canada border. In November 1813, conscious of the British encroachment on Plattsburgh, New York, members of the Vermont militia asked Chittenden to let them intervene. Chittenden declined, though the militia leaders claimed that this was the result of pressure from his advisers.