Oxford, currently sixth in the table, confirmed on Sunday that Wilder's contract has been terminated and financial compensation has been agreed with another side in the same division, rumoured to be Northampton Town.
Wilder guided Oxford back into the Football League via the play-offs in 2010 and has helped the club become established in the fourth tier of English football.
A statement on the club's official website said: "Oxford United confirms that manager Chris Wilder has formally tendered termination of his contract which has today (Sunday) been accepted by the board.
"The club can also confirm that a satisfactory compensation package has been agreed with a League 2 club who are expected to announce Chris as their new manager.
"Assistant manager, Mickey Lewis, has agreed to become caretaker manager with immediate effect and he will be in charge as the first team travel to Exeter City on Tuesday night."
Wilder's last game in charge at the Kassam Stadium was Saturday's 1-0 win over Torquay United, sealed by Deane Smalley's sixth-minute minute.
