The headline profit was generated through the sales of Gary Hooper, Martyn Woolford and Jonathan Forte which offset an annual salary cost of more than £5million.
"Financially, this year under review will appear excellent, but in truth it is a loss of just over £242,000," Wharton wrote in his annual report, sent to shareholders and published on the club's official website.
"The profit has been generated from player sales, most notably Gary Hooper to Celtic back in July 2010. Gary had been fantastic for us and as we pride ourselves in developing successful careers for young players, we went out of our way to help him find the club of his choice."
Relegation to League One means the club miss out on central funding of around £3.7, meaning spending on players will still have to be reduced if the club do not return to the Championship.
"We do have to reduce our operating costs over the next few years unless we can return to the higher league," added Wharton.
Wharton also reiterated his desire to step down as chairman, first revealed in a Q&A with Iron-Bru.net users,saying he is looking for his successor over the course of the season.
"I believe your club deserves a younger and more active chairman to face up to the challenges that lie ahead," he added.
Shareholders will be asked to approve the accounts at the club's annual general meeting, to be held at Glanford Park from 7pm on Thursday December 8.