The 57-year-old former Falkirk, Hibernian, Livingston, Inverness CT and Raith Rovers boss left Ross County in the summer after keeping them in the top flight.
Dunfermline are yet to win in the cinch Championship this season and are four points adrift of Queen of the South at the foot of the table.
Hughes' first game in charge of the Pars is away to Caley Thistle on Saturday.
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