Sometimes, a doctor may prescribe a single dose of the oral antifungal medication called fluconazole (Diflucan). This drug kills fungus and yeast throughout your body, so you may have minor side effects, such as an upset stomach or headaches, after taking it. Your doctor may need to prescribe it if you have a severe infection, and you’d take it for a short time. You shouldn’t take fluconazole to treat yeast infections if you're pregnant, because it may cause miscarriage or birth defects.