He served as a surgeon and physician in the Hospital Department of the Continental Army under General George Washington and other subordinate commanders.

According to Martha J. Lamb, Reverend McKnight received a severe saber cut to his head in the slashing melee that mortally wounded General Hugh Mercer at the Battle of Princeton.

Unable to find an acceptable site for a hospital, the two surgeons took over accommodations in Fishkill, New York, twenty miles north of Peekskill.

Morgan was dismissed as Director General soon thereafter, in January 1777, due to rancor with Washington over supplies and a rampant smallpox epidemic then raging its way through the army.

[16] Isaac Foster took over temporary supervision of the hospitals on the east side of the Hudson River after Morgan's dismissal at Washington's request.

[21] In December 1779, McKnight was in Morristown, New Jersey with Washington,[22] at the encampment near Jockey Hollow, during the worst winter of the Revolutionary War.

[30] McKnight maintained a steady surgical practice and held his professorship until his death from pneumonia,[2] the result of an old war injury,[4] on November 16, 1791 at age 41.

McKnight was interred at the corner of Wall Street and Broadway in Lower Manhattan, just beyond the gates of the historic Trinity Churchyard, next to his wife, Mary, and her father.