I consider Project Quintessence to be primarily science fiction, but it does have fantasy elements. It’s just, the “magic” and golems are given “scientific” explanations, making it more soft sci-fi. And with the modern setting, it’s closer to urban fantasy than fantasy fantasy. A story that was primarily set in Ertiada’s world would be much closer to what people mean when they say “fantasy” without qualifiers; a fictional world that has things that aren’t possible in reality.
I said examples don’t necessarily have to be from anime, and here’s my first one that doesn’t refer to a Japanese series. Though the fact that Avatar: The Last Airbender is anime-influenced isn’t really in dispute.