Charlton were adamant of a long stay in the premiership, however they witnessed an immediate return to the second tier of English football. They narrowly missed out on survival as they finished the season off in 18th place. They were poor in both domestic competitions as they crashed out in the third round of the FA Cup and League Cup, losing to Blackburn Rovers in the FA Cup. They were narrowly knocked out of the league cup, losing 2-1 to a Steve Walsh inspired Leicester City side.
The 1999-2000 campaign saw an immediate return to the top flight for the addicks as they were in emphatic form in the first division. The addicks were in outstanding form through out the campaign, winning the division with ease, gaining 91 points in all matches. They enjoyed a great run in the FA Cup, reaching the quarter finals, only narrowly losing against Bolton. Chris Powell left the club at the end of the season and Graham Stuart made a real impact for the addicks.
Charlton had a real positive return to the top flight during the 2000-01 season as they were emphatic in the division, finishing the season off in a very impressive ninth place, establishing themselves as a fine premiership outfit. They met their London rivals, Tottenham Hotspur, in the forth round of the FA Cup however they were on the receiving end of a thrilling match defeat, 4-2.

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During the 2001-02 season, the addicks new rising young star, Scott Parker, was in emphatic form for the club and the Valliants had now established themselves as a class premiership side, comfortably staying up in the top flight, enjoying a respectable 14th position finish. The addicks reached the last sixteen of the League cup and suffered a narrow defeat against the Hornets of Watford. The narrowly lost an encounter against Walsall in the forth round of the FA Cup, losing the tie 2-1.