The village name 'Winchendon' is Anglo Saxon in origin, and means 'hill at a bend'. Collectively the villages of Upper Winchendon and Nether Winchendon (sometimes called Lower Winchendon) were called Wichendone. The prefix 'Upper' was added later to differentiate between the on higher ground from the village on lower ground.
The ancient manor in the village used to belong to the convent of St Frideswide in Oxford, to whom it was given by King Henry I. Following the suppression of that convent in the early Sixteenth century the manor was given to Cardinal Wolsey, though was seized by the Crown shortly afterwards in 1544 along with Wolsey's other possessions.
In 1623 the manor was given by the king to the Goodwin family, who expanded it into a fine mansion. It then came into the Wharton family, one of whom was made the Duke of Wharton in 1718 for his services to the Crown. He later had all his possessions seized for being a supporter of the Young Pretender (Bonnie Prince Charlie), after which time the manor fell into disrepair and has since been completely demolished.