In March 1996, he was signed by reigning Premier League Champions Blackburn Rovers for £3.5 million, but was sent off on his debut in a 3–0 defeat to Everton. Rovers were relegated to Division One in 1999 and new manager Graeme Souness appointed Flitcroft captain ahead of the 2000–01 season, in which Rovers gained promotion back to the Premier League. Flitcroft continued in his role as club captain for the next three years, but was suspended for Blackburn's 2001-02 League Cup victory although he did lift the trophy with match captain Henning Berg.