The prayer's origin is most likely the Egyptian desert, which was settled by the monastic Desert Fathers and Desert Mothers in the 5th century.
A formula similar to the standard form of the Jesus Prayer is found in a letter attributed to John Chrysostom, who died in AD 407. This "Letter to an Abbot" speaks of "Lord Jesus Christ, son of God, have mercy" and "Lord Jesus Christ, son of God, have mercy on us" being used as ceaseless prayer. However, some consider this letter dubious or spurious and attribute it to an unknown writer of unknown date.
What may be the earliest explicit reference to the Jesus Prayer in a form that is similar to that used today is in Discourse on Abba Philimon from the Philokalia. Philimon lived around AD 600. The version cited by Philimon is, "Lord Jesus Christ, Son of God, have mercy upon me," which is apparently the earliest source to cite this standard version. While the prayer itself was in use by that time, John S. Romanides writes that "We are still searching the Fathers for the term 'Jesus prayer.'"
A similar idea is recommended in the Ladder of Divine Ascent of John Climacus (circa 523–606), who recommends the regular practice of a monologistos, or one-worded "Jesus Prayer". The use of the Jesus Prayer according to the tradition of the Philokalia is the subject of the 19th century anonymous Russian spiritual classic The Way of a Pilgrim, also in the original form, without the addition of the words "a sinner".
Though the Jesus Prayer has been practiced through the centuries as part of the Eastern tradition, in the 20th century, it also began to be used in some Western churches, including some Latin Catholic and Anglican churches.