In November 1848 he became the President of Washington College (now Washington and Lee University) in Lexington, Virginia; he followed Henry Ruffner as president. Junkin's published speeches as president of Washington College include his inaugural address in February 1849 and one at Rutgers College in July 1856. Junkin remained at Washington College until May, 1861, when he resigned the presidency at the age of 71 and moved to Philadelphia amidst controversy regarding his pro-Union views and Virginia's secession from the United States. Confederate General Stonewall Jackson had been Junkin's friend and eventually son in law when Jackson was a teacher at the Virginia Military Institute, which also is located in Lexington. The movie Gods and Generals briefly portrays the poignant end to this friendship, at the start of the Civil War, when Jackson joined the Confederate army (taking one of Junkin's sons with him) and Junkin departed for Pennsylvania. During the War, Junkin wrote a polemical attack on secession, which was also critical of abolitionists. He died in Philadelphia in 1868 and he was later reburied in Lexington, Virginia. His headstone incorrectly indicates that he was the founder of Miami University.