The 1998-99 season was a fine campaign for the Latics, they finished the season off in sixth position, earning the club a play off birth, however they lost to Manchester City in the play offs. They crashed out of the FA Cup in the second round as they suffered defeat against Notts County, losing on penalties. Graeme Jones and Stuart Jones were in outstanding form for the club through out the campaign and the Wigan revolution was only just starting.
The 1999-2000 season saw a further improvement by the club, they were emphatic in the league, finishing the campaign off in forth place, in turn earning the club a birth in the play offs. They beat Millwall in the first round of the play off final; however they suffered heartbreak at Wembley in the play off final, losing against Gillingham 3-2 after extra time. They were poor in the FA cup once again as they could only manage a second round finish in the FA Cup, suffering defeat against Wolves. Arjan de Zeeuw was in outstanding form for the club, coming from Barnsley the previous year.
The 2000-01 campaign saw the Latics once again reach the play offs, this time finishing the second division in sixth position, meeting Reading in the play offs. They lost the encounter over two legs 2-1. They crashed out of the league cup in the second round, losing against Wimbledon. They played remarkably well in the first round of the competition; defeating Scunthorpe United 5-1 on aggregate over two legs.
John Filan arrived at the club in 2001 and immediately established him self as the first choice goal keeper. The 2001-02 season saw a decline in Wigan’s league performances, despite a respectable 10th place finish. Steve Bruce guided the club through out the campaign. The highlight of their season was an incredible 6-1 league victory over Stoke City in November. However, one week after their terrific victory brought about arguably one of their worst results in the 21st century. They met Canvey Island at home in the first round of the FA Cup and lost the match 1-0, it was a game that everybody expected Wigan to win really heavily. The Wigan team of the 2001-02 season included Ian Kilford, Derek Stillie, Simon Haworth and Tony Dinning.