Viduka's debut season at Middlesbrough was initially impressive, albeit frustrated by injuries. In the 2005–06 season however, Viduka was in sensational form in all competitions for Middlesbrough, reaching double figures early on in the season. He also played an important part in spearheading Middlesbrough's campaign in the UEFA Cup where they twice had to score four goals in a game to proceed. They eventually lost in the final to Spanish side Sevilla on 10 May 2006.

With his contract due to expire at the end of the 2006–07 season, Middlesbrough manager Gareth Southgate expressed his interest in keeping Viduka. In August 2006, he was awarded the number 9 shirt at Middlesbrough, his preferred number at all his previous clubs. Following another successful season, in which he scored 19 goals, Viduka attracted interest from other clubs who were hoping to sign him on a free transfer as he became out-of-contract. However Southgate reiterated his wish to retain Viduka's services and revealed he would offer him a new contract. However, Viduka joined north east rivals Newcastle United on a free transfer on 7 June 2007.

Leeds United manager David O'Leary signed Viduka just before the 2000–01 season for £6 million. At Leeds he was expected to line up in a three-pronged attack alongside Harry Kewell and Michael Bridges, but injuries to those two saw him form a partnership with Alan Smith in Leeds UEFA Champions League matches, while Robbie Keane also benefited in their Premiership matches together. In his first Elland Road season, Viduka scored 22 goals, including all four in a memorable 4–3 win over Liverpool at Elland Road. He signed a five-year deal in the summer of 2001.

In the 2002–03 campaign Viduka scored another 22 goals, however Leeds' off-pitch financial troubles prompted the club to sell key players, including Harry Kewell and Robbie Keane. This prompted speculation that Viduka would join the Leeds exodus with Barcelona confirming their interest in the Australian international along with Premiership clubs Liverpool and Manchester United.

With the relegation of Leeds United to the Football League Championship, the sale of Viduka to Middlesbrough was completed.

Celtic bought him in December 1998 for GB£3.5 million. In the same month as his signing Celtic stunned Scottish football by announcing that a stressed-out Viduka had quit the club without kicking a ball for them. A week later Zagreb complained that they had not received their fee for the player. These issues were eventually resolved and Viduka made his first appearance in a Celtic shirt on 16th February 1999, scoring for the under-21 team as an over-age player in a 4–2 victory against Motherwell.He was voted Scottish Premier League Player of the Year after scoring 27 goals in his first full season at Celtic Park. He was regarded as a skilled player, able to hold the ball up well and bring other players into the game.

In 1995 he moved to Croatia to play with Croatia Zagreb, where he stayed for three years and made an appearance in the UEFA Cup. The grandstand at Knights' Stadium, home of the Melbourne Knights was renamed the Mark Viduka Stand in his honour and paid for with his transfer money.