Sir Thomas was the son of Sir Richard Windebank of Hougham in Lincolnshire and his wife, Margaret, the daughter of Griffith ap Henry. He owed his fortunes largely to his Lincolnshire neighbour, Sir William Cecil, who secured his appointment to the fourth stall in Worcester Cathedral in 1669 and sent him, as a travelling companion, to his son, Thomas (afterwards Marquis of Exeter). Many of Windebank's letters, describing his vain efforts to keep his charge straight and teach him French, and their travels in France and Germany during 1661 and 1662, are extant in the Public Record Office. He also took every opportunity of sending his patron lemon trees, myrtle trees and tracts on canon and civil law. After his return, he was made clerk of the signet, and occasionally acted as clerk of the Privy Council. He continued his friendly relations and correspondence with Lord Burghley until the latter's death and, afterwards, with Sir Robert Cecil. He was knighted by James I on 23rd July 1603, settled at Haines Hill in St. Nicholas Hurst (Berkshire) and died on 24th October 1607. He married Frances, younger daughter of Sir Edward Dymoke of Scrivelsby in Lincolnshire, by whom he left one son, Sir Francis, and three daughters. Of the latter, Mildred (d. 1630) married Robert Reade of Linkenholt near Andover in Hampshire, and was 3x great grandmother of President George Washington.