Fate most likely isn't human. Let's go over what we know here...
1. His barrier is definitely not a human technique.
2. Eva identified him as "probably not human", some sort of puppet or creation.
3. He uses EXACTLY the same spells as Hermann (That old guy who Negi and Kotaro fought when Kotaro first came to the academy) : The water teleportation, petrification, Eternal Petrification.
4. Fate himself said "Since I have never needed training..." This might mean he was created with that knowledge of advanced spells and martial arts.
5. Both he and Asuna appear to be part of the war 20 years ago- Most likely, Asuna was placed in a stasis field of some sort for 20 years to safeguard the rest of the magical world, just in case they tried to use her powers to destroy the world again. Fate may have been placed in a stasis field too, OR as an alternative, he might be a creation, meaning he can live as long as he is not destroyed.