She acted again in Philadelphia, Here I Come! in 1994, on Broadway, opposite Robert Sean Leonard. It would be her final Broadway appearance. Her first had been 40 years earlier, in the 1957 staging of Dylan Thomas' Under Milkwood. Other Broadway credits included God and Kate Murphy (1959), Step on a Crack (1962), Antigone (1971), The Crucible (1972), The Plough and the Stars (1973), The Innocents (1976), The Father (1981), Medea opposite Zoe Caldwell (1982), Steaming (1982), Corpse! (1986) and Lost in Yonkers (1991). In the early 1970s, she frequently appeared with the Repertory Theatre of Lincoln Center.
She also performed with the O'Casey Theatre Company in Shadow of a Gunman and Three Shouts from a Hill.
Ms. Flanagan won a 2001 Olivier Award, the London version of a Tony, for her performance in Dolly West's Kitchen—an honor she called the high point of her long career.
In a recent interview, she attributed her confidence as an actor to having been raised in a happy family in which both parents were elected town mayors. "I grew up totally adored and admired. My mother taught me that I could do anything I wanted to; she knew I was strong in myself."