The first mention of the name Clongowes Wood occurs in a Close Roll of King Henry IV, dated 24 February 1418. The reference is to the dowerlands of Anastasia Wogan, the widow of Sir David Wogan of Rathcoffey, as the the "third part of the Silva de Clongowes, in the western part therein, that is to say forty acres". Just a century earlier, the Rathcoffey estate had reverted to the Crown. It had first been held by Adam de Hereford, a young friend of Strongbow, who had come to Ireland with him. In 1317 Edward II granted these lands to Sir John Wogan, who was at that time a Lord Deputy in Ireland.

The name Clongowes Wood comes from a hybrid of Latin and Irish Silva de Clongowes: silva= the wood; cluain= the meadow; gobha= the smith. Thefore the wood of the meadow of the smith or Coill Chluana Gabhann.