After Euro 1996, Brøndby received a transfer fee of £1.65 million, when Nielsen moved to England to play for FA Premier League club Tottenham Hotspur. He played nearly 100 league matches for Tottenham, and he was a pivotal player when the club won the 1999 League Cup. In the final minute, he scored a diving header to give Tottenham a 1–0 win against Leicester City, and Nielsen was subsequently honoured as "Man of the Match". Following controversies with Tottenham manager George Graham, Nielsen moved down a league in March 2000, when he was loaned out to Wolverhampton Wanderers in the English First Division in a three-month deal. During his time at Tottenham, he represented the Danish national team in five games at the 1998 FIFA World Cup, scoring a single goal against South Africa, as well as in two games at the Euro 2000 tournament.