Wilson was born in Paisley, Scotland, the son of an illiterate distiller. In 1779 he was apprenticed as a weaver. His main interest at this time was in writing poetry, and his poems commenting on the unfair treatment of the weavers by their employers got him into trouble with the authorities. The "golden age of Renfrewshire song" is embodied in the persons of Wilson and Robert Tannahill. Robert Burns was eight years older than Tannahill. He was born near the Hammils, a broad if not steep waterfall in Paisley where the River Cart skirts Seedhill. It does indeed appear to be the case, as William Motherwell states, that a great amount of literary activity began in Paisley around this time.
In May 1794 Wilson left Scotland with his nephew to find a better life in America. Wilson obtained employment as a schoolteacher in Milestown, near Philadelphia. In 1801 he left Milestown and found a new teaching post in Gray's Ferry, Pennsylvania; Wilson took up residence in nearby Kingsessing. It was here that he met the famous naturalist William Bartram who developed Wilson's interest in ornithology. In 1802 Wilson decided to publish a book illustrating all the North American birds. With this in mind he traveled widely, watching and painting birds and collecting subscribers for his book. The result was the nine-volume American Ornithology (1808-1814), illustrating 268 species of birds, 26 of which had not previously been described. He died during the writing of the ninth volume, which was completed and published after his death by his friend George Ord. Wilson lies buried next to Ord at Gloria Dei Church cemetery in Philadelphia, Pennsylvania.
Wilson is now regarded as the greatest American ornithologist prior to Audubon. It was his meeting with Audubon in Louisville, Kentucky in 1810 which probably inspired the younger man to produce a book of his own bird illustrations.
Several species of bird were named for Wilson, including Wilson's Storm-petrel, Wilson's Plover, Wilson's Phalarope and Wilson's Warbler. The warbler genus Wilsonia was also named for him by Charles Lucien Bonaparte.
The Wilson Journal of Ornithology is named after him.