Thomas was born on June 18, 1805, on Walton, New York as the final child of Charles and Elizabeth Stockton however his mother died at childbirth and his father refused to raise him, leaving him adopted by one of his mother's sisters, living with Dr. and Mrs. T. B. Whitmarsh until when Thomas left for the United States Military Academy in 1822.

[1] Stockton, though an infantry officer, was renowned for his topographical skills and was a major contributor to the construction of several military roads and bridges in Detroit.

[2] Due to Stockton's inheritance of land from his father-in-law in Flint, he resigned from the United States Army in 1836[2] and became a civil engineer and began improving the harbors at Ohio, Indiana and Michigan as part of the projects on the Great Lakes.

[2] Returning home to Flint, Stockton donated 20 acres of his southern portions of his holdings for the upcoming Michigan School for the Deaf and in 1850, Rowland Ferry, John Cage and Stockton formed the Genesee County Agricultural Society to promote agriculture, horticulture, household and mechanical arts within Michigan.

When Stockton returned to Michigan he formed a militia company, the Flint Union Greys, in preparation for the American Civil War.