The students started off the new millennium on a low under Scottish coach Jim BoneThe Club finished in a disappointing 13th place in the league. But with the installment of former South African goalkeeper Roger de Sa as new head coach at the start of the 2001/02 season, the team’s fortunes changed once again, as they were lead to a strong 7th place finish in the PSL.
The Wits youth policy continued to roll out young talents. Midfielder Stanton Fredericks and goalkeeper Rowan Fernandez were soon on the shortlists of South Africa’s most famous club, Kaizer Chiefs, and were sold to Chiefs in mid-2001. Midfielder Josta Dladla was also receiving attention for his remarkable playmaking prowess, and was eventually sold to Danish Premier League club AGF Aarhuis at the end of the 2001/02 campaign.
In 2002, the club announced that the Bidvest Group would be taking over sponsorship of the club, while Danish company Hummel would take over as technical sponsor. Later that year, midfielder Stanton Fredericks made his first appearance for South Africa, and joined only a handful of players to have scored on debut for Bafana Bafana. Meanwhile, defenders Ashley Makhanya and Tony Coyle both earned their first caps for the national team.
The 2002/03 season turned out to be one of Wits’ best ever campaigns with ‘The Clever Boys’ going on a run of 14 league matches unbeaten over the New Year period to eventually finish third on the PSL table. The side also saw several players receive national call-ups including the club’s brilliant center-back Tony Coyle and promising midfielder Benson Mhlongo.
In 2004 Benson Mhlongo and Neil Winstanley represented the club in the Africa Cup of Nations, Group D. After another strong third place finish in 2003/04, it seemed the clubs fortunes were looking up, only for a dismal 2004/05 campaign to see the side relegated to the Mvela Golden League De Sa's ultra-defensive tactics, coupled with a mass player exodus at the start of the season, saw the side score just 24 goals in 30 league matches to finish bottom of the league. De Sa was then replaced by former Santos and Maritzburg United coach Boebie Solomons, assisted by former Bafana Bafana midfielder Eric Tinkler. The Solomons-Tinkler combination restored order to the ranks and the Clever Boys managed to secure the Mvela Golden League title, and an immediate return the country’s top flight after starting the season with six successive victories.
In June 2007 Roger De Sa rejoined the club after a two-year absence. He replaced caretaker Eric Tinkler who had succeeded Boebie Solomons during the 2006-07 season. Roger De Sa’s return saw the Clever Boys moving up the log only to return right where he found them.
During the 2007/2008 season The Clever Boys started to get back into the game moving from 13 th place to 12 th . Within a season the Clever Boys were back at it, finishing in 6th place. However during the 2009/2010 season things went down south once more as they finished in 10 th place, only to return to 6th again in the 2010/2011 season.
The Clever Boys won the Nedbank Cup in 2010 which opened Soccer City before the 2010 World Cup. The finals saw Bidvest Wits and Amazulu going head to head.