Running works the muscles and stresses the joints. Inflammation is your body’s way of healing irritated or injured tissue, which is why you’re sore after running or working out. Ibuprofen (Advil) and Naproxen (Aleve) are non-steroidal anti-inflammatory drugs (NSAIDs). They reduce inflammation in the tissues and joints. Patients who are taking anticoagulants or have a history of GI issues should not take NSAIDs without discussing with their doctor first, as they do have the potential side effects of thinning the blood and irritating the stomach, among others.