Thigpen was best known for playing The Chief on the PBS game shows Where in the World Is Carmen Sandiego? and Where in Time Is Carmen Sandiego?, as well as voicing the role of Luna on Bear in the Big Blue House. Her other television appearances included a regular role on The District and guest roles on All My Children, Spenser: For Hire (with Avery Brooks), LA Law, Law & Order, and Homicide: Life on the Street.
Thigpen also appeared in numerous Broadway and Off-Broadway productions, notably The Night That Made America Famous, Tintypes, Fences, Boesman and Lena (for which she won her first Obie Award), and An American Daughter (for which she won a Tony Award). Her first feature film role was in a musical theatre adaptation, Godspell, though most of her further roles in films such as The Warriors, Tootsie, Lean on Me, Naked in New York, Bicentennial Man, and Shaft did not call upon her singing ability.
Beyond her work on Cacophony, Thigpen was a prolific narrator of audiobooks, including adaptations of titles by Maya Angelou, Octavia E. Butler, Ernest J. Gaines, Zora Neale Hurston, Toni Morrison, and Ann Petry. She served a similar function when she read The Salamander Room by Anne Mazer on Reading Rainbow (hosted by LeVar Burton).
Lynne Thigpen Elementary School in Joliet, Illinois was named in her honour.