Speaking after the U's 1-0 win over Torquay United on Saturday, chairman Ian Lenagan said that he understood that Wilder had quit the club and that he was on the verge of taking charge at Northampton Town.
However, Wilder's agent, Iain Wood of New Era Global Sports, told Sky Sports News that Lenagan was wrong.
"Following on from various comments in the media we can confirm that Chris Wilder has not resigned as manager of Oxford United Football Club either verbally or in writing and therefore continues in his role," read a statement from Wood.
"There have been numerous discussions over the past few days in regards to Chris's position and a link to Northampton Town Football Club. However as confirmed by the Oxford United Chairman in the local media following the game on Saturday, Oxford United have been fully part of these discussions.
"Chris feels strongly he has acted with integrity in this situation, as he has throughout his five years at Oxford United. Further comment will only be made as and when appropriate."
Wilder has been Oxford manager since December 2008.