After the war Herndon returned to Tyler, where he resumed his legal practice in partnership with Judge John C. Robertson and began to specialize in railroads. He served as counsel for a number of lines, on the board of the Tyler Tap line, and as vice president of the Kansas and Gulf Short Line Railroad. He was elected from the First Congressional District to the United States House of Representatives of the Forty-second Congress in 1871 in a closely contested election and served until 1875. He attended a number of Democratic national conventions and is said to have engineered the nomination of Winfield Scott Hancock for president at the Cincinnati, Ohio, convention in 1880. In 1892 Herndon was one of the leaders of the opposition to James S. Hogg. Herndon died in Albuquerque, New Mexico, on October 11, 1903, and is buried in Oakwood Cemetery, Tyler.
32° 21.216, -095° 18.520