Sheffield-born Wilder, 46, a veteran of one game for Northampton on loan in 1998, served his managerial apprenticeship with Alfreton Town and Halifax Town before taking on the Oxford job at the end of 2008. During his time there he took the U's back into the Football League from the Conference before twice missing out on the League Two play-off places.
His future at the Kassam Stadium, however, has been in some doubt since the end of last season when he was handed a new one-year contract by chairman Ian Lenagan.
It was Lenagan who claimed on Saturday that Wilder had resigned, a claim initially disputed but then formally confirmed on the Oxford United website on Sunday evening.
A compensation package has been agreed between the two clubs and Wilder's focus shifts straight away from the chase for the top six to avoiding the drop out of the Football League after signing a three-and-a-half year contract.
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