The Saints finished the 1998 – 1999 season in a disappointing 17th position and could not drastically improve it the following year as they finished it off in 16th place.
The Saints met Aston Villa in the fourth round of the FA Cup and league during the 1999 – 2000 campaign; however they lost on both occasions against the Midlands club.
Southampton made a decent improvement in the premiership during the 2000 – 2000 campaign as they finished off the season in a top half finish of tenth position. Chris Marsden and Marain Pahars were in fine form for the Saints through out the campaign. The Saints reached the fifth round of the FA cup, meeting Tranmere Rovers and after the match finished all square in the first match, the replay proved to be a thriller as the score line ended 4-3; however Tranmere Rovers was the team who scored the four goals in the match.
The Saints enjoyed a decent campaign during the 2001 – 2002 league season as they finished of the campaign in eleventh position in the premiership. They were knocked out of the FA cup in third round as they suffered defeat against Rotherham united in the cup competition.