The charge relates to an incident involving Arsenal defender Ashley Cole in United's 2-0 win at Old Trafford, which ended the London club's unbeaten Premier League run after 49 matches.
Van Nistelrooy has to admit or deny the charges by Tuesday, with the case due to be heard on Thursday.
Arsenal manager Arsene Wenger has also been asked to explain his comments about Van Nistelrooy and match referee Mike Riley, and the FA said it was investigating alleged incidents in the tunnel after the game.
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