Cygnet's first season included Hedwig and the Angry Inch, Bed and Sofa, and Fully Committed.
Highlights in the first eight seasons include Cat on a Hot Tin Roof, The Little Foxes, The Invention of Love, Yellowman, Copenhagen, Fences, A Little Night Music, The History Boys, Noises Off, Sweeney Todd, The Norman Conquests, Cabaret, and the World Premiere of Stephen Metcalfe's Tragedy of the Commons.
Since its founding in 2003, Cygnet Theatre has presented at the Old Town Theatre in Old Town San Diego State Historic Park.
On November 16, 2022, NTC Foundation and Cygnet Theatre announced they would be partnering to create the Joan and Irwin Jacobs Performing Arts Center.
The project, which costs $38.9 million, will be located in Building 178 at Liberty Station and is scheduled to open in the fall of 2024.