He played three national team games under national manager Richard Møller Nielsen, until his national team career went on a hiatus in September 1991. In November 1990, he was sold to French club Lille OSC, in a Lille club record transfer deal. Frandsen joined fellow Danish international Jakob Friis-Hansen at Lille, and played four years at the club. While at Lille, he represented Denmark at the 1992 Summer Olympics, where he played full-time in Denmark's three games before elimination. When Lille faced economical difficulties in the summer 1994, Frandsen returned home to Denmark to play for F. Copenhagen (FCK).
He was included in the Danish squad for the 1998 FIFA World Cup, where he was used as a substitute in two games. In September 1999, Frandsen joined Bolton's league rivals Blackburn Rovers for £1. 75 million. The decision was against the wishes of Bolton manager Colin Todd, who subsequently resigned. Frandsen's stay at Ewood Park for Blackburn was far from happy.
He failed to settle at the club, and at the end of the season he returned to Bolton for £1. 6 million. In his final year at Bolton, the club reached the 2004 League Cup final, though they were beaten 2–1 by Middlesbrough. He played 304 first team games for the club in all competitions, scoring 38 goals in the process. Frandsen left Bolton Wanderers to join Wigan Athletic on a free transfer in June 2004, helping them get promoted to the Premiership, scoring once in the process against Brighton.  After playing well in his first time at the club, he received a severe cruciate ligament injury and he decided to retire in January 2005.
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He soon earned a reputation as one of the best players in English football playing outside the top-flight FA Premier League championship, and it was assumed that it would only be a matter of time before one of the bigger clubs came in for him. Instead, he helped Bolton win promotion back to the Premier League in the 1996–97 season. Frandsen's national team career was revived in November 1996, when he was recalled by new national manager Bo Johansson, after more than five years of absence from the Danish national team. He was one of the few bright spots of Bolton's second Premier League campaign, which ended in swift relegation back into the Football League.
Frandsen stated his intention to only play in Denmark temporarily, and having won the 1995 Danish Cup with FCK, he moved abroad once again in August 1996. He was sold to English club Bolton Wanderers for £1. 25 million. Playing in the second tier of English football, he made his debut for the club in a 1–1 draw at Port Vale before scoring his first goal for Bolton in the following game against Manchester City.
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