I am having the same problem with my rabbit. He has to take medication for ringworm and absolutely hates it! He has taken a medication called metacam, which he loved, so it was easy to give it to him, but now I am having trouble with the new stuff.
A good suggestion I have heard is to put something “tasty” on the tip of the syringe so your rabbit will be more likely to take the medication. I am going to put a little bit of natural applesauce on my bunny’s syringe next time to see if that helps. You can also try smearing some banana on it. Another thing you can do is keep a snack near you for afterwards so your bunny will have something to look forward to. That might help make the experience a little less horrible for her. It might be hard (as I know) to do, but you can try to hold her mouth shut as soon as you can get the medicine in so less will end up all over the place. My bunny kept moving his head and backing away, so quite a bit got all over his fur too and he started frantically cleaning himself…. Next time I hope it will turn out better…
Good luck with your bunny! I am hoping my next attempt with my bunny will go well too. 