After the ectopic pregnancy surgery, you may experience pain and discomfort for a few weeks. In the case of ectopic pregnancy treatment with medicines, you may experience episodes of abdominal cramps for a week or two. Other occasional side effects (affecting up to 15 percent of women) include nausea, vomiting, indigestion, mouth ulcers, sensitivity to light, or feelings of fatigue. The feeling of a pregnancy ending can also cause emotional outbursts in many women.