Thomas Russell Bowden was born on May 20, 1841, near Williamsburg, the son of Lemuel J. Bowden and Martha Ellen Shackelford Bowden, and grew up on one of his father’s farms. In 1859 he entered the College of William and Mary, where he studied Latin, Greek, French, history, and economics for two years. As a member of the college’s Phoenix Literary Society, Bowden won a gold medal for his debating skills. He probably also studied law in his father’s Williamsburg office.
Bowden’s father and his uncle Henry M. Bowden were uncompromising Unionists during the winter of 1860–1861. In the spring of 1862, after the Union army occupied Williamsburg and acquired responsibility for the patients in the Eastern Lunatic Asylum, Union officers appointed Henry Bowden clerk and steward of the institution and made Thomas Bowden collector of its pay-patient fund. With the withdrawal of the Union army later in the summer the Bowden family left Williamsburg, and the events of the Civil War made its members Republicans. Bowden’s father represented Virginia in the United States Senate before his death on January 2, 1864, and Bowden’s sister later married Charles H. Porter, a Union army officer from New York who was a member of the Virginia Convention of 1867–1868 and served two terms in Congress from Virginia.