Azathioprine (Imuran) is an immune system-suppressing drug, meaning that it can theoretically halt the attack of the immune system on your nerves. Mild sickness and headaches are quite common on starting azathioprine (or after an increase in dose). These settle in most people after a few weeks. These settle in most people after a few weeks. Some people develop more severe sickness and vomiting with azathioprine. In Summary. Commonly reported side effects of azathioprine include: infection, nausea, leukopenia, and vomiting. See below for a comprehensive list of adverse effects. Summary. Headache is found among people who take Azathioprine, especially for people who are female, 50-59 old , have been taking the drug for 1 month, also take medication Humira, and have Rheumatoid arthritis. Uses. Azathioprine is used to prevent organ rejection in people who have received a kidney transplant. It is usually taken along with other medications to allow your new kidney to function normally. Consumer information about the medication AZATHIOPRINE - ORAL (Imuran), includes side effects, drug interactions, recommended dosages, and storage information. Read more about the prescription drug AZATHIOPRINE - ORAL. Azathioprine will be prescribed for you by a specialist doctor. Swallow the tablets with plenty of water, after a meal. Do not crush or break the tablets. Your headaches should subside when your body gets used to the higher mg's. I still get headaches but not nearly as bad and truthfully, I don't even think they are from the 6mp to be honest - more like tension headaches. I find that Tylonel Arthritis helps since is has a higher mg then extra strength Tylonel. Azathioprine is used with other medications to prevent transplant rejection (attack of the transplanted organ by the immune system) in people who received kidney transplants. BOXED WARNING. WARNING - MALIGNANCY. Chronic immunosuppression with Azathioprine, a purine antimetabolite increases risk of malignancy in humans. Reports of malignancy include post-transplant lymphoma and hepatosplenic T-cell lymphoma (HSTCL) in patients with inflammatory bowel disease.