He had two spells at Wigan as a player and turned down a new contract to stay at Fratton Park.
Caretaker boss Graham Barrow has left the DW Stadium after relegation from the Championship last season.
Second-bottom finished nine points adrift of safety after winning just ten games and scoring only 40 goals in their 46 games.
Portsmouth, in contrast, had a ten-point cushion from fourth-placed Luton in League Two and topped runners-up Plymouth on goal difference.
Warren Joyce will be succeeded as the Latics manager by Pompey chief Paul CookAP:Associated PressWarren Joyce was caretaker boss at the DW Stadium as Wigan went downPA:Press AssociationPaul cook won the League Two title and boss of the year award with PortsmouthReutersPaul Cook knows Wigan are fancied for a quick return to the ChampionshipPA:Press Association
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