Jedediah Hotchkiss was born November 30, 1828, in Windsor, New York. His father was a farmer but appreciated Jedediah's studious bent enough to enroll him at Windsor Academy. Young Hotchkiss was fascinated with geography and geology, and after graduation in 1846 he and several friends made a walking tour of Lyken's Valley in Pennsylvania. There Hotchkiss took his first job, teaching a term of school. When that was finished, his further wanderings brought him to the Luray Valley, part of the Shenandoah Valley of Virginia. There he again took work, first as a tutor to a local family and then as principal of his own Mossy Creek School. Having been raised a Presbyterian, he joined the local Presbyterian church and in December 1853 married Sara Ann Comfort of Lanesboro, Pennsylvania. In 1859 the couple moved to a farm near Churchville, Virginia, where, together with Hotchkiss's brother Nelson Hotchkiss, they opened the Loch Willow Academy. The school was highly successful. It was during these years that Hotchkiss, who still enjoyed the study of terrain, taught himself mapmaking.

When the Civil War began, Hotchkiss—despite his and his wife's background and his brother's staunch Unionism—sided with the Confederacy and in June 1861 entered the Confederate army. His first service came in what was later to become West Virginia. In the Confederate debacle at Rich Mountain, Hotchkiss successfully led a small contingent of Confederate troops in escaping capture at a point when Union forces had them nearly surrounded. Later that summer Confederate general Robert E. Lee arrived in western Virginia. Quickly recognizing Hotchkiss's special skills, he put him to work making a map of Tygart's Valley. By autumn 1861, however, Hotchkiss was suffering from typhoid fever and had to take an extended sick leave.

Returning to duty in March 1862, Hotchkiss sought and gained assignment as a topographical engineer on the staff of Stonewall Jackson. On March 26, Jackson gave Hotchkiss his famous order: "I want you to make me a map of the Valley, from Harpers Ferry to Lexington, showing all the points of offense and defence in those places." Hotchkiss did just that, preparing an accurate, detailed, and easily understandable map for Jackson's use. Using pencils of different colors, he took great pains to make the map clear and easy to grasp, and he frequently briefed Jackson on aspects of terrain.

During the Shenandoah Valley Campaign of March and April 1862, Hotchkiss performed invaluable terrain reconnaissance and appreciation duties for Jackson. After the campaign he continued in those duties with Jackson's Second Corps of the Army of Northern Virginia throughout the Virginia campaigns of 1862 and 1863. At Chancellorsville in May 1863 Hotchkiss was not far from where Jackson was mortally wounded by friendly fire. The same volley that eventually killed Jackson also killed Hotchkiss's friend and tent-mate, Captain James Keith Boswell.

Hotchkiss continued his duties as a topographical engineer with the Second Corps under its subsequent commanders, Richard S. Ewell and Jubal A. Early. He accompanied the Army of Northern Virginia in its invasion of his wife's native state, and he was with Early when the Army of the Valley marched to the outskirts of Washington, D.C., in 1864. That autumn, information Hotchkiss provided was a key factor in the Confederates' initial success at the Battle of Cedar Creek. The following spring, Hotchkiss continued to serve in the upper Shenandoah Valley area with generals Thomas L. Rosser and Lunsford Lomax. Upon learning of Lee's surrender at Appomattox Court House on April 9, 1865, Hotchkiss conferred with Confederate secretary of war John C. Breckinridge before disbanding his small topographical detachment and returning to his home, where he gave his parole to Union forces on May 1, 1865.

After the war Hotchkiss taught for several years and then quit teaching to take up engineering full-time. He became an avid promoter of and investor in the development of mining and timber interests in western Virginia and neighboring West Virginia. He composed the Virginia volume—volume 3—of the set Confederate Military History (1899). Living in Staunton, he was for many years active in the Second Presbyterian Church. Hotchkiss died January 17, 1899 at his home, the Oaks.