K.P.
It's safe for babies as young as 6 weeks. My son took it, no side effects. Every med has potential side effects, but they are not common. I would, however, wait until she is over her stomach bug to start it! You can give her yogurt, but I haven't heard of yogurt "curing" thrush...maybe it could help prevent it, but you wouldn't want your daughter to suffer by trying alternative therapies that "might" work. Like bacteria, yeast strains are becoming resistent to medication. I would give her the medication the doctor prescribed, and use it as directed.