In April 1863, he led a brigade under Stonewall Jackson. Because he knew Colston from the time when both were professors at VMI, Jackson recommended Colston to lead a division. At the Battle of Chancellorsville on May 2, Colston led one of the divisions involved in Jackson's flank attack on the Union army's right flank. His division was placed in the second line on May 3. In the two days fighting, his division lost 31% casualties. However, on May 3, "Raleigh Colston, the least experienced of Lee's generals of division, proved painfully slow in directing his men into action." Lee relieved Colston of command of the division on May 20. In November 1863, his cousin Raleigh T. Colston, an 1850 VMI graduate who had become colonel of the 2nd Virginia Infantry (also part of the Stonewall Brigade), became one of the few fatalities of the Battle of Mine Run.