Your provider can treat babesiosis with a combination of medications. These include antiprotozoals, antibiotics and antimalarial drugs. They might give them to you through an IV in your arm or in pill or liquid form for you to swallow. If you’re very sick, you may need other procedures, like a blood transfusion, to get better. Medications used to treat babesiosis Your provider might treat you with a combination of these medications: Atovaquone. Azithromycin. Clindamycin. Quinine.