Headache After B12 Shot: 3 Effective Strategies to Feel Better Vitamin B12 deficiency, sometimes called cobalamin deficiency, happens when your body is either not getting enough or not absorbing enough vitamin B12 from the foods you eat. Vitamin B12 is an important Vitamin B12 deficiency can cause symptoms like headaches, fatigue, depressive mood, gastrointestinal issues, and more. While vegetarians are at a higher risk of vitamin B12 deficiency, it can affect non vegetarians too. Check Persistent Headaches? You Could Have a Vitamin B12 Deficiency