Calcium Buildup (Hypercalcemia): High amounts of vitamin D cause the body to absorb more calcium. If blood calcium levels get too high, it frequently triggers headaches, nausea, fatigue, and frequent urination.Magnesium Depletion: The body requires magnesium to metabolize large amounts of vitamin D. A high daily intake can deplete magnesium stores. Because magnesium deficiency is a well-known trigger for migraines, this drop can cause severe headaches.