The Reds sit 17th in League One, seven points clear of the relegation zone and seven points behind the play-off places.
Wilson, appointed in December 2013, was unable to keep Barnsley up last season, but it was hoped a concerted push would be made for promotion this time around.
A failure to do so led to the Oakwell board acting yesterday and placing senior development coach Paul Heckingbottom and Academy chief Mark Burton in charge.
Wilson was joined by assistant Chris Hutchings in leaving the club.
Several names have been linked with the post, including former player Craig Hignett, but chief executive Ben Mansford has revealed that, as yet, no interviews have been lined up.
He added: “We will seek to get someone who can realise the supporters’ aspirations, which is Championship football back at Oakwell at the earliest opportunity.”
Barnsley tomorrow travel to bottom club Crawley Town, beaten 5-0 by Doncaster Rovers on Tuesday night, before hosting Crewe Alexandra a week later.
Wilson, who famously led the Reds into the Premier League in his first spell, lost 31 of his 63 games in charge.
A board statement said: “Recent performances and results have been concerning, considering the club currently boasts the fifth-highest wage bill in League One in addition to a fourth-highest equity donation by our owner.
“Meanwhile, our current League position of 17th is in stark contrast to an average home gate of sixth-best in the division.
“Whilst the club acknowledges there has been a large turnover of players, the league position is still unacceptable considering all of the above.”
One manager already in employment who has distanced himself from the vacancy is Neil Redfearn.
Hugely popular in his playing career at Oakwell, the 49-year-old is enjoying a decent run of form as Leeds United head coach.
Redfearn said: “I am enjoying the position here and the opportunity I have been given. This is a massive club.”