My rheumatologist prescribed 20mg prilosec once A day to help coat my stomach from so many NSAIDS. I am able to drink coffee again and tolerate moderately spicy foods. Although methotrexate can cause stomach upset both with the oral tablets and injections, it does not specifically cause gastritis. In my experience, the stomach problems with methotrexate tend to occur when the drug is first started. Summary. Upset stomach is found among people who take Methotrexate, especially for people who are female, 60+ old , have been taking the drug for 1 month, also take medication Humira, and have Pain. Methotrexate can cause serious or life-threatening side effects. Tell your doctor if you have diarrhea , mouth sores, cough, shortness of breath, upper stomach pain, dark urine, numbness or tingling, muscle weakness, confusion, seizure, or skin rash that spreads and causes blistering and peeling. Doctors give unbiased, trusted information on whether Methotrexate can cause or treat Abdominal Pain: Dr. Kumar on methotrexate stomach pain: Prevacid (lansoprazole) is usually a well-tolerated medicine. However, any medicine can cause side effects in some people. If you suspect the side effects are due to Prevacid (lansoprazole), your options are either to switch medicines or to stop it. Methotrexate is a powerful medication that can be used for many serious conditions. MTX is an antineoplastic (anticancer) drug that is used in protocols to treat all kinds of cancers such as leukemias, lymphomas, and breast cancers. The most common side effects for methotrexate are stomach upset and fatigue and you've experience both. Taking a new medication can be a bit of a shock to the system and one of the ways I usually. Stomach Upset Take methotrexate after meals, which may reduce the risk of stomach upset. If you develop nausea or vomiting, report it promptly because another medication may be prescribed to control these symptoms. Does anyone else on Methotrexate have trouble with your stomach? I feel awful. I bought some probiotics today to see if that would help. I am bloated and burping a lot. I was extremely unwell, with severe stomach pain but it was put down to the sulfrazalizine and it was stopped. As I don't have any other symptoms it was decided I was tolerating the methotrexate well.