Well, that can depend on many things!
For one thing, it can depend on whether you prefer taking your medications through your mouth or by another route. Some people have a hard time swallowing their oral medications. Other people may not like being injected with a needle.
But in terms of how well methotrexate works in treating a condition, taking a drug orally may affect how your body absorbs it. Drugs that are taken by mouth have to pass through the stomach and small intestine to be absorbed. Drugs that are injected do not have to go through this system—so more medication may be absorbed into the body to do its job.
Clinical studies have shown that patients given subcutaneous methotrexate through an auto-injector pen were able to absorb more of the drug—and experienced fewer gastrointestinal side effects—than patients given methotrexate tablets.