Jonathan Alper was an American theatre director and actor. After graduating from Amherst College in 1971, he stuided theatre at the Webber-Douglas Academy in London. He made his acting debut in 1974 at the Arena Stage in Madness of God. He went on to be the director and literary manager at the Folger Theater. After leaving Folger, he went to New York, where he directed plays Off-Broadway at theatres including Playwrights Horizons and the Manhattan Theatre Club. He earned an Obie award for directing a production of Safe House at MTC. He became MTC's literary manager in 1980 and then an artistic associate in 1984. During his time at the theatre, he developed and presented new plays by British and American playwrights, including works by Beth Henley and Terrence McNally. 

Jonathan Alper passed away in 1990. After his death, Manhattan Theatre Club created a directing fellowship in his honor.