After an early leading role in Peter Greenaway's cult success Drowning by Numbers, her first major role in front of a mass audience was as Joanna Farley in a 1989 television episode of Poirot, the Agatha Christie-based detective series. She later appeared as a fictional Finnish princess, Anna, in the 1991 comedy King Ralph. Two years later, she appeared as Lady Chatterley in a television drama of the same title.

In 1996 she played the fashion designer Anita in the popular Disney film 101 Dalmatians opposite Glenn Close as Cruella de Vil. In 1998, in the popular television drama The Echo, she played sultry Amanda Powell. The next year, she played in the sci-fi/horror movie Event Horizon as Lieutenant Starck, executive officer of the research and rescue ship Lewis & Clark, sent to rescue crew of the long-thought-lost experimental ship Event Horizon.

One year later she played opposite Mel Gibson in the successful film, The Patriot loosely based on the American Revolution, Joely plays Charlotte the family aunt. Later that year she was modelling a necklace, when director Charles Shyer noticed her resemblance to doomed 18th-century royal Marie Antoinette. Thus, she secured the role of that queen in the 2001 film The Affair of the Necklace.

Also in 2000 she played the lead in Ben Elton's movie adaptation of his own book "Inconceivable" renamed "Maybe Baby" opposite Hugh Laurie.

In 2003, she took on the major role of playing Julia McNamara in the controversial television drama Nip/Tuck based on the lives of two dysfunctional plastic surgeons in Miami. Her mother appeared in several episodes.