On television, she played Dr. Lenara Kahn in the episode "Rejoined" in Star Trek: Deep Space Nine (1995), the Borg Queen in three episodes of Star Trek: Voyager (1999–2000), Karen Sammler on the drama series Once and Again (1999–2002), and Moira Queen on the series Arrow (2012–2020).

One of Thompson's most controversial television appearances was on an episode of Star Trek: Deep Space Nine titled "Rejoined".

She made a guest appearance on Law & Order: Special Victims Unit on October 7, 2003 in the season five episode "Mother", as Dr. Greta Heints, a psychiatrist who rehabilitates sex offenders to prepare them to return to society.

[1] In November 2006, she made her first appearance as Army Lieutenant Colonel Hollis Mann on the CBS series NCIS, in the recurring role of Agent Gibbs' love interest.

In 2009, Thompson starred on the short-lived NBC series Kings, based on the biblical story of David, as Queen Rose Benjamin, an analogue of Ahinoam, the wife of Saul.