Caravaggio’s Saint John the Baptist (Rome, Galleria Borghese) was painted in 1609–1610 for Cardinal Scipione Borghese, the nephew of Pope Paul V, and although many scholars have carefully studied and analyzed it in the last decades, the meaning of this unusual image has not been fully revealed. This present article focuses on the parable of the Good Shepherd related in the Gospel of St John (10, 11–21) as a key to the reading of particular aspects of Caravaggio’s work, and interprets its depiction as a visual message conveyed to Cardinal Borghese that the artist strongly wished a pardon from the Pope for the murder that he had committed on 28 May 1606.