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With a small profit made before depreciation and an inject of £60,000 through the share release the clubs borrowings were reduced by over £200,000.
In his report to shareholders included with the report, Wharton repeated his intention to resign and offered support for his successor Chris Holland.
He said: "There is still no room for complacency but this is certainly an acceptable performance, and I would suggest creditable given the current circumstances.
"To my successor Chris Holland and the board, I wish them continued success and thank them most sincerely for the support they have given me over the past two years.
"I have every confidence that they will continue to improve the club whilst keeping careful control of the finances.
"It is no easy task, but Scunthorpe United is that bit special and deserves to progress while others may lose ground under the present difficult conditions.
"When I step down at the AGM I will miss the close involvement with the management and the players. Not only do they provide the football skills, but they also create a vibrant and exciting atmosphere in and around the club.
"Brian Laws is one of the best managers in the Football League and in his six years in charge he has never become complacent and is always striving for ways to improve every aspect of the club."
In the previous financial year Scunthorpe United had recorded a loss of £81,139.