It is the first time in six years that the club have turned in a profit, with the sum considerably different to the £7.2m net loss they reported 12 months ago.
The figures cover the 2011-12 season which ended with the Latics in 15th place, with turnover up from £50.5m to £52.6m.
Wigan said on their official website that while salaries remain their biggest expense, they had trimmed them from £39.9m to £37.7m, with £10.4m spent on new players. The sale of Charles N'Zogbia to Aston Villa meant they brought in £7.9m of profit on player sales.
The club's debt, including borrowings and loans from chairman Dave Whelan and his family reduced to £20.5m from £72.2m, with £48m of it converted into equity.
"The results are once again encouraging and we are very pleased to report a net profit position in a very competitive environment," said chief executive Jonathan Jackson.
"By increasing turnover and controlling costs the club is continuing to progress to a break-even operating position which all football clubs are aspiring to but many are finding it difficult to achieve."