The 1990-91 campaign was not a great one for the Latics supporters. They reached the third round of the FA Cup, crashing out after losing against top flight club, Coventry City. They witnessed a significant improvement in their league fortunes as they finished the season off in a respectable 10th position. Peter Atherton was in outstanding form throughout the season and he left the club for Port Vale before playing for Sheffield Wednesday, a club he would go on to become captain at. The 1991-92 season saw a gradual decline in Wigan’s league fortunes and they finished the season off in a disappointing 15th place. Phil Hughes played well in goal for the club; however it was a poor campaign. The Latics reached the third round of the FA Cup as they met top flight club, Notts County, they lost the match 2-0.
The 1992-93 campaign proved to be dark times for the club as they suffered a miserable campaign that saw the club only manage a 23rd position finish, in turn relegating the club back to the forth tier of English football, a place they had not been for 11 years. They suffered a heavy thrashing in the league cup, losing a second round tie against Ipswich Town 4-0.
Wigan’s fortunes took a turn for the worse during the 1993-94 season and finished a miserable campaign in 19th place in the third division, narrowly avoiding a relegation battle to stay in the football league. The club were also eliminated out of the FA Cup in the third round, losing 1-0 against Gillingham.