Some common side effects of this Prograf medication include: Shaking, Headache, Diarrhea, Nausea, Vomiting, Loss of appetite, Upset stomach Keep in mind that your doctor has prescribed you this medication because its benefits to you are greater than the risk of side effects. Many people who use this medication do not have serious side effects. However, if you experience any of the following serious side effects as mentioned below, visit your doctor right away. Mood changes, Dizziness, Signs of kidney problems, Shortness of breath, Hearing problems, Pounding heartbeat, Yellowing of eyes or skin, Severe leg pain