Educated at the University of Edinburgh, where his father was professor of mathematics, Stewart began teaching there when he was 19. In 1775 he took over his father's chair and 10 years later was appointed professor of moral philosophy, a position he held until 1820.

As a student, Stewart had come under the influence of the works of the Scottish realist Thomas Reid (Reid, Thomas), particularly An Inquiry into the Human Mind on the Principles of Common Sense (1764). Stewart, like Reid, held that philosophy should be a scientific discipline unfettered by metaphysical speculations and categories, though he objected to some of Reid's formulations of his new science of mind. Stewart's affinity for the scientific approach to philosophical problems is reflected in his mathematics career, and he often made analogies between the axioms of mathematics and the laws that govern human thinking.

Stewart's major work is Elements of the Philosophy of the Human Mind, 3 vol. (1792, 1814, and 1827). His other works, which fill an 11-volume edition (1854–58), include Outlines of Moral Philosophy (1793), Philosophical Essays (1810), and Philosophy of the Active and Moral Powers of Man (1828).