Our checkout page. Fluconazole will not treat a viral infection such as the common cold or flu. It is little inexpensive in nature. Diflucan is usually taken by mouth as a one-time only dose, with or without food, or as directed by your doctor. Fluconazole has been associated with birth defects when given at high doses early in a pregnancy. If you have a vaginal infection, do not have sex until you have finished your treatment.