He revealed his departure at a press conference on Monday, after appointing Brian Laws as manager for his third stint following the sacking of Alan Knill.
He has been looking for a successor for the past two years, without success, and has now set a deadline for his exit.
It means he will step aside in June, at the end of the club's financial year.
"For me I am not looking to make any money out of it, I would rather give them to somebody if it helped, I just want to find somebody to carry on," said Wharton.
"I will do whatever is best for the club and whatever I can. I don’t particularly want to sell the club. When you say sell the club, I don’t actually own it, but I have a fairly sizable share holding."
The club are expected to announce a loss of close to £2million for the last financial year, with another loss expected this season.
So against the background of the club losing around £30,000 a week, Wharton warned the club still faces further cuts unless investment is brought in.
"We lost a lot of money last year and are on course to do the same this year, you tell me how you survive unless you get your costs down to match your income," he said.
"I don’t believe that anybody can survive on losses unless you can find somebody coming in who is willing to throw money away. You have to match outgoings and incomes, that’s what we have got to do going forward.
"I have put a loan in place so that if I leave at the end of the year then they are sound when I go. That is repayable over 20 years, but after this year they have to find a way of balancing the books."
The Iron Trust, the club's supporters trust, said they were keen to work with the current board of directors or any new investor.
“We do not yet know what the future holds for Scunthorpe United from the summer, but hope that it can include a strong supporters voice in a central role," they said in a statement.
“We believe fans who back that ideal could make a big difference by joining the Iron Trust, as this would give the concept of supporter involvement a real mandate at our club.
“We look forward to working with the current board, and any potential new investors, to help the club move forward."