What's the correct way to say it?
Do I have to take the medicine?
Yes,you do OR Yes,you have to

Question

Answer

I agree with Mathias and Abhi: follow the grammar of the question if in doubt.  "Yes, you have to (take it)."

That said, "yes, you do" is still a common and perfectly acceptable response.

Answer

yes you have to

Answer

I was said to use the same kind of thing that is used in the question. Here the question has "have to". So, in the answer also "have to". Refer to Matias' answer.

Answer

Both are fine.