As stated before in the introduction, after helping Booth with his leg injury he was paid 25 dollars for his services. Within days Dr. Mudd was under arrest by the United States Government. He was charged with conspiracy and with harboring Booth and Herold during their escape. Dr. Mudd was found guilty. His sentence was life imprisonment. He missed the death penalty by one vote. Dr. Mudd was imprisoned at Ft. Jefferson in the Dry Tortugas which is 70 miles from Key West.
Dr. Mudd was allowed to stay in mail contact with his wife. Mrs. Mudd also wrote letters to President Andrew Johnson for her husband to be released. He tried to escape and failed on September 25, 1865. In February of 1867, Dr. Mudd was assigned to the prison's carpentry shop. In the summer of 1867, yellow fever broke out on the island. After the fort's physician died on September 7, Dr. Mudd took a leadership role in aiding the sick. Dr. Mudd, himself, came down with the disease but recovered. Because of his outstanding efforts, all noncommissioned officers and soldiers on the island signed a petition to the government in support of Dr. Mudd.
Dr. Mudd was released from Ft. Jefferson on March 8 and arrived home on March 20. He had served somewhat less than four years in prison. He partially regained his medical practice and lived a quiet life on the farm. On January 10th, 1883, Dr. Mudd died of pneumonia at the age of 49. He was buried in St. Mary's cemetery next to the Bryantown church where he first met Booth in 1864.