Diego Neria Lejarraga, who underwent a sex change to become a man, visited the Pope at the Vatican on Saturday with his female partner, Spanish newspaper Hoy reported.
The man had previously written to the Pope complaining of feeling marginalized by the Catholic Church in his home town of Plasencia, Estremadura, after having a sex change.
According to Lejarraga, who is a practising Catholic, he was rejected by his parish and the priest had called him “the daughter of the devil”.
The Pope then rang Lejarraga twice in December last year before Christmas, before inviting him to the Vatican.
“The first call was already much more than I had expected,” Lejarraga told the paper.
“By the second [phone call] I still couldn’t believe what was happening to me, because I know that my case is nothing. There are so many people suffering in this world who do not deserve the attention of the Pope.”
They finally had a private meeting at 5pm on Saturday at Saint Martha's House in the Vatican.
The Vatican has so far declined to comment.
The news comes in spite of a poll conducted in 2014 which revealed that Spanish people are the least homophobic out of a total of 40 nations.