One of the earliest extant sources for the Joan legend is the De septem donis Spiritu Sancti (“The Seven Gifts of the Holy Spirit”) by the 13th-century French Dominican Stephen of Bourbon, who dated Joan's election c. 1100. In this account the nameless pontiff was a clever scribe who became a papal notary and later was elected pope; pregnant at the time of her election, she gave birth during the procession to the Lateran, whereupon she was dragged out of Rome and stoned to death.

The story was widely spread during the later 13th century, mostly by friars and primarily by means of interpolations made in many manuscripts of the Chronicon pontificum et imperatorum (“The Chronicle of the Popes and Emperors”) by the 13th-century Polish Dominican Martin of Troppau. Support for the version that she died in childbirth and was buried on the spot was derived from the fact that in later years papal processions used to avoid a particular street, allegedly where the disgraceful event had occurred. The name Joan was not finally adopted until the 14th century; other names commonly given were Agnes or Gilberta.

According to later legend, particularly by Martin (who dated her election in 855 and who specifically named her Johannes Angelicus), Joan was an Englishwoman; but her birthplace was given as the German city of Mainz—an apparent inconsistency that some writers reconciled by explaining that her parents migrated to that city. She supposedly fell in love with an English Benedictine monk and, dressing as a man, accompanied him to Athens. Having acquired great learning, she moved to Rome, where she became cardinal and pope. From the 13th century the story appears in literature, including the works of the Benedictine chronicler Ranulf Higden and the Italian humanists Giovanni Boccaccio and Petrarch.

In the 15th century, Joan's existence was regarded as fact, even by the Council of Constance (Constance, Council of) in 1415. During the 16th and 17th centuries the story was used for Protestant polemics. Such scholars as Aeneas Silvius Piccolomini (afterward Pope Pius II) and Cardinal Caesar Baronius regarded the story as unfounded; but it was the Calvinist David Blondel who made the first determined attempt to destroy the myth in his Éclaircissement familier de la question: Si une femme a été assise au siège papal de Rome (1647; “Familiar Enlightenment of the Question: Whether a Woman Had Been Seated on the Papal Throne in Rome”). According to one theory, the fable grew from widespread gossip concerning the influence wielded by the 10th-century Roman woman senator Marozia and her mother Theodora of the powerful house of Theophylact.