He was born Thomas Fairfax of Walton and was presumably a supporter of the House of York in the Wars of the Roses. Fairfax's original home was near the Battle of Towton, which decided the outcome of that war. From 1489 to 1492, he successfully claimed the ownership of the Gilling Estate during two inquisitions. Before Fairfax, the de Etton family had owned this estate. However, in 1349, Margaret de Etton, the sister of Thomas de Etton—who owned the estate at that time and erected its tower keep—married Fairfax's ancestor, also named Thomas Fairfax. She entered an agreement that, should the de Etton family fail, the estate would be inherited by the Fairfax family. Thus, historian John Marwood wrote that "it could be argued that the rightful heirs had at last come home." When Fairfax received the estate, he became the Fairfax of Walton and Gilling.