Diego Neria Lejarraga met the pontiff on Saturday after writing to him in December to complain he was being treated as an outcast in his parish in Plasencia in western Spain, according to the Spanish daily Hoy.
The 48-year old, who has undergone sexual reassignment surgery, told Francis in the letter that he was treated poorly by parishioners and one priest had even called him "the devil's daughter."
The Argentine pontiff, known for calling people unannounced, rang Lejarranga on Christmas Eve and set up the meeting, which took place on Saturday but was kept off the official calendar, the report said.
The Vatican would neither deny nor confirm the meeting took place.
Officially the Church does not recognise sex changes but its current leader has urged it to show greater compassion towards sections of society which have felt excluded from its embrace, most notably when he said of homosexuals, "Who am I to judge?"