With that said, it is possible to effectively treat toenail fungus with the help of professional doctors. There are also a lot of factors patients can contribute with in helping speed up its healing and recovery period. A number of individuals take dietary supplements and vitamins to aid with their treatment program. Here are the top vitamins you should take for toenail fungus treatment. Vitamin B3. Since toenail fungus primarily affects your nails, it is important to provide them with adequate amount of nutrition to keep them strong.