The song (sung in character by Donald Fagen) concerns a young runaway woman who has fled her abusive home life in Florida and who is now involved with the narrator, an older, affluent New York man. It begins as an apparently straightforward love song, with the narrator extolling the virtues of his new love ("the wonderwaif of Gramercy Park"). In the middle verse - which name-checks upmarket grocery store Dean & Deluca - Janie and the narrator evidently act out a role-playing scenario in which the narrator imagines himself to be Frank Sinatra in 1959, with Janie as a showgirl that Sinatra seduces.
The final verses take on a darker, more coercive tone - the narrator suggests that they go for a weekend away to his friend Binky's "sugar shack" in Pennsylvania, although he also hints that "Janie" may in fact be underage ("Or would that be a federal case?"). The final verse reveals that the narrator intends to bring along another woman for a menage a trois ("Who has a friend named Melanie, who's not afraid to try new things?") and implies that the narrator's continued interest in Janie is dependent on her agreeing to the tryst ("Who gets to spend her birthday in Spain? Possibly you - Janie Runaway.")