With his new position, Stokes moved to Fort Gibson in the Arkansas Territory (now part of the state of Oklahoma) and advocated for the Cherokee, Seneca, Shawnee, and Quapaw tribes. He died in November 1842 and is buried near Fort Gibson. Stokes is believed to be the only soldier of the American Revolutionary War buried in Oklahoma. In 1943, a United States Liberty ship named the SS "Montfort Stokes" was launched. She was scrapped in 1962. Stokes first married Mary Irwin and they had one daughter. After his wife died, he married Rachel Montgomery (1776–1862) and they had five sons and five daughters. His son, Montfort Sidney Stokes, fought as major in the Mexican–American War and died in 1862 in the Civil War as colonel of the 1st North Carolina Infantry Regiment.