they have the same meaning but 아파요 is more formal then 아파. Thanks!

There are another expressions in Korean that's similar to formal or informal in English. You can distingish that '아파' is informal and '아파요' is formal simply. But the difference of those two language is the meaning of '아파요' include a bit of being plite. So you can use the word '아파' to your friend in your ages or under, and also you can use the word '아파요' to your parents or someone older than you or someone you've never met before even though they're younger than you.