Stewart was a co-founder of Queen's Medical School and remains one of the most memorable figures in Queen's history. He was born in Perth, Scotland and educated at the University of Edinburgh, where he received his medical license in 1834. He immigrated to Canada shortly thereafter and set up as a surgeon in Kingston in the early 1840s.
He played a leading part among local doctors in persuading Queen's Board of Trustees to set up a medical school in 1854 and was the university's first Professor of Physiology and Anatomy. He delivered the first-ever lecture in the Faculty of Medicine in 1854.
Stewart was the owner, editor, and chief contributor to the Kingston Argus, a small newspaper that served mainly as a vehicle for his strong opinions. He was initially the de facto leader of the medical school, but was in constant conflict with colleagues and published attacks against them in the Argus.
He was dismissed from Queen's in 1862 after bitterly opposing an appointment at Kingston General Hospital supported by most of his peers. Despite his temper and opinions, Stewart was widely regarded as an excellent teacher and a caring doctor; his efforts on behalf of the sick and dying in Kingston's devastating typhus fever epidemic of 1847 are a matter of local legend.