The play premiered at the Whitefriars Theatre in December 1609 or January 1610, acted by the Children of the Queen's Revels, led by Nathan Field (who may have played True-wit or Dauphin). Little heed is now given to Fleay's hypothesis that Jonson himself played Morose. Jonson hinted to Drummond that the play failed; he mentioned certain verses calling the title appropriate, since the audience had remained silent at the end. A report from the Venetian ambassador shows that at least one person spoke up in response to the play: Arbella Stuart, who complained of a personal reference to a recent intrigue involving the prince of Moldavia. Whatever trouble this complaint may have caused Jonson was apparently covered over by Stuart's subsequent marriage to William Seymour. That the play remained current is suggested by a Stationer's Register entry in 1612 which indicates the intention to publish a quarto of the play.
The play influenced at least two minor plays before the interregnum: Peter Hausted's Rival Friends (1631) and Jaspar Mayne's The City Match (1639).
After the Restoration, Epicœne was frequently revived and highly appreciated; in the course of a lengthy analysis, Dryden calls it "the pattern of a perfect play." Samuel Pepys's diary records several viewings of the play. The first, in early summer of 1660, seems likely to have been among the first plays performed after Charles II's return to London. Pepys saw the play again in January 1661, with Edward Kynaston in the title role.
In 1664, Pepys saw the play at the Theatre Royal with Elizabeth Knepp in the title role; this was probably the first performance in which a woman played Epicœne. Over the next century, a number of celebrated actresses, including Anne Oldfield and Sarah Siddons, performed the part. Siddons, however, was directly associated with the play's departure from the stage. David Garrick and George Colman's updated version (1752), featuring Siddons, was a disastrous failure. Bonnell Tyler, echoing Reformation comments on the play, condemned Morose as ludicrously unnatural, and other reviewers were no kinder. Garrick replaced Siddons with a boy, responding to historically ill-informed complaints that a female Epicœne was ludicrous. The revamped casting did not save the production, and Epicœne vanished from the boards for over a century, a victim of the general collapse in popular taste for non-Shakespearean Renaissance drama.
In 1935, Richard Strauss's opera Die schweigsame Frau, with a libretto by Stefan Zweig based on Jonson's play, premiered in Dresden.