The U's called a Thursday morning press conference on the subject of Wilder's future, leading many to question whether the 45-year-old would be leaving the Kassam.
But chairman Ian Lenagan ended speculation by confirming that Wilder will manage the club in League Two next season.
"I am fully aware that some supporters, some might say the majority, were expecting a different decision, " he told the Oxford Mail.
"We are convinced that in Chris Wilder Oxford United has a young manager of high promise.
"It became clear early this season that our injury situation was a mountainous obstacle to overcome this season."
Wilder added: "I'm delighted to be reappointed. I'm honoured to be manager. I take full responsibility for Oxford United falling short in our points tally this season."
Wilder has has been with Oxford since 2008 and led them to promotion from the Blue Square Premier, but an injury-hit campaign will end with them finishing in mid-table.