What is the treatment for secondary dysmenorrhea that is best and has fewest side effects?

Anti-inflammatories. Secondary dysmenorrhea is usually due to a physical problem like endometriosis, uterine fibroids or polyps. Medications like advil or Aleve (naproxen) (non-steroidal anti-inflammatories= nsaids) can help and usually have little side effects. In general it is better to treat the cause if it is secondary dysmenorrhea. Primary dysmenorhea is usually hormonal and responds well to nsaids.