Born in Charlottesville, Virginia, he was the youngest son of former CSA Colonel Charles C. Wertenbaker and his wife Fanny (the former Frances Thomas Leftwich).
He barely knew his grandfather, William Wertenbaker (1797-1882) who was the second librarian of the University of Virginia, according to his gravestone appointed to that office in 1826 by former President Thomas Jefferson, who founded the university. The boy's name (as well as that of an uncle) honored that link. Grandfather Wertenbaker built three houses on his property located between the university campus and Charlottesville's town center, which was developed into the Wertland Street Historic District after his death. Although by the time of this boy's birth, his father was involved in agar manufacturing and his only brother living at home was a salesman, his father was involved in Confederate memorials, having been colonel of a Virginia Infantry unit during the Civil War, and several relatives also fought for the Confederacy in the conflict.
According to the dust jacket of one of his books, Torchbearer of the Revolution (1940), Wertenbaker was descended from one of Bacon's followers in Bacon's Rebellion "who had the distinction of being the first native-born Virginian to be hanged in Virginia." However, he fails to specify the ancestor's name, and the book mixes history and historical fiction. The Library of Virginia has made available online several notes by lawyer and author Samuel Bassett French, who died before completing a planned biographical dictionary, about members of his family, including this man's birth near Milton outside of Charlottesville, the furthest navigable point on the James River, and from where bateaux conveyed tobacco downriver to Richmond. His grandfather William Wertenbaker fought in the War of 1812, then by 1840 owned 14 slaves in Albemarle County,reduced to eight slaves in 1850. In the last census before the Civil War and abolition of slavery, William Wertenbaker owned nine enslaved people, ranging from 64 and 54 year old women to 14, 12 and 10 year old boys and 8 year old and 8 month old girls.
According to another of his books, The Shaping of Colonia Virginia, T.J. Wertenbaker attended private schools including Jones' University School before graduating from Charlottesville Public High School and beginning studies at the University of Virginia in 1893. Wertenbaker interrupted those studies in 1900-1901 to teach at St. Matthew's School in Dobbs Ferry, New York before returning to the University of Virginia and receiving Bachelor's and Master's degrees in 1902. He became an editor of the Charlottesville Morning News and the Baltimore News before re-entering the University of Virginia as a graduate student in 1906, and continued those studies while also teaching as an Assistant Professor of History at Texas Agricultural and Mechanical College beginning in 1907. He became an instructor in the University of Virginia's history department in 1909 and completed his thesis and received his PhD degree the following year. Wertenbaker later received honorary degrees from several universities in the United States and abroad.
