Jose Baltazar Hernandez Molina was a minister at a church in the north-western state of Baja California when he started seeing the girl.
The 31 year old is accused of killing her when she left him for a boy her own age.
According to the Mirror newspaper Mexican Deputy Against Organised Crime, Miguel Angel Guerrero, said the pastor had admitted killing the girl because he was jealous but now felt sorry.
He said: "He has been charged with murder and rape because the girl was underage. We are also investigating who else knew about his relationship and why they did nothing."
If found guilty he could be jailed for 50 years.