Compounded Methylcobalamin (Vitamin B12) Injection, 5mg mL Vitamin B12 Injections: Benefits and Risks Understanding Headaches from B12 Deficiency 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 Ear Nose and Throat An ENT's Guide to Understanding Headache Issues After Botox Experiencing any of these symptoms? B12 supplementation might be right for you. Some causes of low B12 are diet, alcohol use, certain diseases like Chrohn's and Celiac Disease, and Gastric Bypass surgery,