Abert was born in Shepherdstown, Virginia (now West Virginia). He graduated from West Point in 1811, but declined a commission to practice law. After leaving West Point, he married Ellen Matlack Stretch in January 1812. He enlisted in the D.C. Militia during the War of 1812, and rejoined the army as a topographical engineer with the rank of brevet Major in October 1814. His son, James William Abert, who also became a member of the corps, was born in 1820. In March 1829 John Abert was appointed to the leadership of the corps, and promoted to Colonel in July 1838. Officers working under him were responsible for the exploration and mapping of the lands west of the Mississippi River. He was elected an Associate Fellow of the American Academy of Arts and Sciences in 1845. He retired from the Army in September 1861. Abert died in Washington, D.C., and was buried in Rock Creek Cemetery.