Charles McKnight left study under William Shippen to join the Continental hospital service in 1775. He worked in the Cambridge hospitals during the siege of Boston and accompanied the army's medical establishment into New York. During the difficult retreat of 1776 he helped care for sick soldiers at North Castle and establish hospital accommodation at Fishkill. He faced shortages of medicines, surgical supplies and buildings and disputes among senior physicians.

In April 1777 McKnight became surgeon general, also described as senior surgeon, of the Middle Department's Flying Hospital. This was a particular wartime hospital appointment, distinct from the later office of Surgeon General of the U.S. Army. After the Hospital Department was reorganized in 1780 he served as chief hospital physician in the Middle Department, leaving military service in 1782.

McKnight subsequently developed a New York practice and taught anatomy and surgery at Columbia College from 1785. He also held the post of port physician and became a regent of the University of the State of New York. His surgical reputation included work as an oculist; a surviving notice records his training of William Stillwell, who later performed eye surgery in New Jersey. He published an account of an operation for an extrauterine pregnancy that attracted attention in Britain. His career joined military hospital administration with the revival of medical teaching and specialized surgery in postwar New York.