After returning to Canada, Martin married Ellen Hill, or "Karakwineh" (meaning "moving sun"). He also enrolled in the Toronto School of Medicine in 1863. He graduated with his B.M. in 1865 and his M.D. in 1866. In 1866, he also served in the Queen's Own Rifles during the Battle of Ridgeway, one of the armed conflicts of the Fenian Raids from the US of that year.