The Apostle Thomas was already considered the founder of Christianity in India by the time of Prester John's Letter. However, it is significant that the Letter not only mentions St. Thomas but uses the legend of Thomas as a geographical marker to help delineate his kingdom. Notably, the Apostle Thomas is named in all three of the Prester John texts that predate the Letter.

Each text mentions Thomas's tomb, which according to medieval lore had two resting places: Edessa and India. The particular qualities of this usage remind the reader that despite John’s kingdom’s exotic locale, this land can indeed claim a legitimate and recognizable Christian forebear (even if we don't really know where to find him).

One of Jesus's original Twelve Apostles, Thomas (popularly known as Doubting Thomas) was sent by Jesus to preach the Gospel in the Eastern parts of the world. By the Middle Ages, Thomas was a very important figure for several Eastern sects of Christianity, made popular by the Gospel of Thomas and the Acts of Thomas (late 3rd century).

More generally Thomas was a very important figure for Nestorian Christians and, beginning in the twelfth century, the Syriac Acts of Thomas, a key source for the Letter, was just beginning to circulate in the Latin West. 

The location of the tomb of St. Thomas, an important feature of the Prester John legend, was very much in dispute in a the Middle Ages. A number of medieval travelers claimed to have visit the site. Marco Polo observes that there existed an Christian community devoted to St. Thomas as far east as Mylapur, India, the city where Polo places Thomas' tomb.