Nystatin (a non-systemic anti-fungal medication) and Diflucan, Nizoral, Lamisil, and Sporanox (systemic anti-fungal medications) are effective therapies for individuals with chronic candida and other yeast infections - including children on the autism spectrum. The difference between the two groups has to do with absorption and overall effectiveness.
Nystatin is considered a local anti-fungal medication, i.e. local to the digestive system. It does not get absorbed into the blood stream (or at least to any significant degree) and therefore has its effect locally to yeast inside the digestive system. I equate Nystatin to Pepto-Bismal. Pepto-Bismal coats the stomach, while Nystatin coats the intestinal tract. Therefore, in order to get maximal benefit it needs to be dosed multiple times throughout the day because the coating wears off quickly. Because it does not get absorbed it can be taken for prolonged periods of times (months, and in some cases years) without requiring blood work to check for liver function stress.
Diflucan (along with Nizoral, Lamisil and Sporanox) are all systemic anti-fungal medications. This means they have some effectiveness in the digestive system, but they also get absorbed into the bloodstream and have more of a systemic effect on yeast throughout the body. There half-life is longer than Nystatin and only need to be dose once, and sometimes twice daily. However, because these medications do get absorbed into the bloodstream and are metabolized through the liver periodic blood work (every 2 months) is necessary to evaluate liver function.
Both groups of anti-fungal medications are effective, and can play a role in anti-candida therapy for children on the autism-spectrum who have difficulties with chronic yeast issues.