The Premier League side have managed to sell just 20,000 of their 31,000 tickets for Saturday's clash and the match could have the lowest attendance for an FA Cup semi-final since Wembley became the permanent home of the semi-finals in 2008.
The record low for a semi since then was the 75,064 that watched Stoke beat Bolton in 2011, and a similar crowd is expected despite Championship side Millwall being on the brink of selling their 31,000 tickets.
Wigan have averaged crowds of 18,996 in the Premier League while Millwall's average crowd in the Championship has been 10,516.
Wigan boss Roberto Martinez looked to put the club's relatively poor support into context.
"It's not about the numbers," Martinez said. "The numbers need to have a meaning. Back in 1995, when I arrived at the football club, we had gates of 2,000 people.
"Now we are in the best league in the world, and we are in the semi-final of the best cup competition - for us to take whatever figure it is represents an incredible percentage of the town.
"It's an incredible turnaround of the fans we had 15 years ago, so for us it is a success."
Jason Taylor, a committee member of the Wigan Athletic Supporters' Club, also defended the number of fans his club are taking to Wembley.
"Our supporter base has grown phenomenally over the last 15 years," he said.
"If you go back in history our crowds have gone from 1,200 to 15,000.
"They are continuing to grow but we are still a long way behind Manchester United, Liverpool and Everton, who have a lot of fans in the town.
"We have already sold more than our average attendance and we have only got around 12,000 season ticket holders, with around 25% of those aged under 16.
"So even if we sell 20,000 tickets then we have sold thousands more than usual."
Despite the shortfall, the FA are going to great lengths to try and get the ground as full as possible.
A neutral section holding 6,000 fans has been set up where fans can purchase tickets for £30.
They will enter via a separate section to the Wigan and Millwall fans and club colours will not be permitted.
The FA says the section will "ensure that the FA gives more football fans, England and FA Cup fans, the opportunity to attend a game at Wembley."
Some 1,500 tickets have also been made available to British army troops.
The FA had announced just days ago that the FA Cup was enjoying its best attendances in 30 years in reference to fifth and sixth round ties.
What's your view – have Wigan done well to sell 20,000 tickets for a small club in a rugby league town? Or is 10,000 empty seats a poor showing from a Premier League club? Leave your thoughts below…