Thomson shared her first lead in Stealing Heaven (1988) with Derek de Lint and Denholm Elliott. In its review, Films and filming said "Kim Thomson's Heloïse moves with delicate poise, a heroine worthy of Rossetti or Burne-Jones, with vivacity and intelligence. The next year, 1989, she played Estella in a film of Great Expectations directed by Kevin Connor, with Jean Simmons, who had played Estella in the 1946 film, as Miss Havisham. Also in 1989 she was Cordelia on stage in King Lear, directed by Jonathan Miller, with the British Theatre Yearbook commenting "Kim Thomson's Cordelia can rarely have been equalled; she was exquisite in beauty, tender in care, full of youthful integrity."

In 1992, Thomson was the leading lady of the TV series Virtual Murder, and in 1994 played another leading role in a costume drama series, The Wanderer. Dozens more appearances in film and on television followed, often as a character Actress, such as her role as a society reporter in The Princess Diaries 2: Royal Engagement (2004).

In 1997, she took on the part of Lady Chiltern in An Ideal Husband, of which the Theatre Record said "Others have played this pure, cool, idealistic, demanding role with more authority and finesse, but she is simply right for it". In 2001, she was Irina in a new West End theatre production of Uncle Vanya directed by Peter Gill.

During 2008 Thomson had a recurring role in ITV's detective show The Bill, as barrister Naomi Woods, wife of DC Jacob Banks.

In March 2009, she became a regular cast member of the ITV1 soap opera Emmerdale, playing the role of Faye Lamb. At the end of 2009, she signed a new contract with the show. In January 2011, it was reported that she was leaving the show and would make her on-screen departure later in the year.

In 2010, Thomson graduated from the University of London with a degree in politics, philosophy and history..