He first came to England towards the end of the 1997-1998 season when moving to Sheffield Wednesday from Portuguese club S.L. Benfica, who signed him from Tirsense in 94/95, when the "jesuítas" stood one win away from a UEFA Cup position. Whilst at Hillsborough he became a huge favourite with the Wednesday supporters who nicknamed him "The Wall" due to his physical presence and powerful style - which was recovered from his stint at Tirsense. Thome scored twice for Wednesday, once against Stockport County in the FA Cup and once against Wimbledon in the league.
In late 1999, with The Owls staring at the prospect of possible relegation in the face, he made the move to Chelsea for a fee of £2.7 million. He was to remain at Stamford Bridge for just nine months, as he found it hard to break up the tried and tested central defensive partnership of Marcel Desailly and Frank Leboeuf. Just one game into the 2000-2001 season Thome was sold to Premiership rivals Sunderland A.F.C. for a fee of around £4 million, quite a considerable profit for the Londoners. He was replaced by Winston Bogarde, a move widely regarded as one of the most disastrous transfers of all time. The sale of Thome was reputedly not sanctioned by Chelsea manager Gianluca Vialli who left the club a short time later.
During his time at the Stadium of Light, Thome struggled with injuries and Sunderland were reluctant to extend his contract. A clause in his contract with Sunderland meant that a considerable sum had to be paid to Chelsea after he played 50 matches. Sunderland were not willing to pay the extra appearance based fee, hence their reasons for not playing Thome towards the end of the 2002-2003 season, a campaign which ended in relegation heartbreak. Thome scored twice for Sunderland, netting in league games against Coventry City and Aston Villa.
In August 2003 he joined ambitious Bolton Wanderers on a free transfer, and became a regular campaigner for The Trotters as they finished in a healthy position in the Premier League, also reaching the final of the Carling Cup where they eventually lost to Middlesbrough at Cardiff's Millennium Stadium. He was offered fresh terms to extend his stay with Bolton, but instead chose to move down a division to their near neighbours Wigan Athletic along with former team mate Per Frandsen.
This proved a good move for Thome as The Latics where promoted to the Premiership for the first time in their history in 2005. However, Thome was loaned out to Derby County in November 2005 and was released from his contract at Wigan on 7 February 2006.
Thome then decided to go to Japan to join Vissel Kobe, who were relegated to second division J2 as it finished at the bottom of the table in 2005 season.
Thome retired after the end of the 2007 season.