"It is alleged the club failed to ensure its players conducted themselves in an orderly fashion," the FA said in a statement.
Leicester have until April 12 to respond to the charge.
Midfielder Aaron Mooy scored the penalty for Huddersfield but Leicester went on to claim a convincing 4-1 victory.
(Reporting by Hardik Vyas in Bengaluru; Editing by Christian Radnedge)
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