In 1969, aged 19 years, Lythgoe auditioned for the BBC’s Young Generation dance troupe, which included her future husband Nigel among its members. Bonnies success as a choreographer of dance productions within the West End led to a career as a producer/director of various theatre productions, including pantomimes. She produced/directed and choreographed the Christmas 2006 version of Peter Pan, starring Henry Winkler, in Wimbledon and Cinderella, starring Patrick Duffy, in Woking.
Lythgoe came to American public attention as a producer and judge on season one of the reality television series So You Think You Can Dance. She also served as one of the judges on So You Think You Can Dance Australia prior to its cancellation in July 2010.
In 2016, Lythgoe was a contestant on the second season of the Australian version of I’m a Celebrity…Get Me Out of Here!, lasting 3 weeks. Her charity of choice was Olivia Newton-John’s Cancer and Wellness Centre.