In this day and age, it's hard to be too careful.

If I were in your situation, I'd keep a standing rule:
No kids in my flat without express prior parental permission, unless there's an imminent emergency (like an angry drunk) and then only until the emergency passes. Keep a log of when minors come and go.

Now, for this kid:
I'd keep his parents in the loop. If possible, I'd make sure he got express permission to be over each and every time he visited. If that's not possible (say, the parents don't care enough to be bothered), then I would get general permission from them, make sure they had your phone number, and make sure he tells his parents where he was each time he goes home. I would also keep a log of when he left and arrived each day. If possible, I would make sure he only goes in rooms that have a window, and keep the blinds open when he is there.

The more "open" you are the less likely any false accusation will be taken seriously.

Also, if he isn't in your apartment for a specific purpose, I would consider relocating. If he's just there to "hang out" with you, consider hanging out in a public place, at church, or at his home, with his parents. Again, this will make any false accusation much less credible.