In recent years, functional endoscopic sinus surgery (FESS) has improved the treatment of sinus disorders. However, various orbital complications have been reported, including optic nerve damage, orbital hemorrhage, infection, lacrimal drainage system injury, and strabismus. Complications are rare but may cause severe morbidity. We describe two patients who underwent endoscopic sinus surgery procedures that resulted in trauma to the medial rectus muscle. The first patient had medial rectus paresia due to contusional trauma and showed spontaneous resolution in a month. The other patient had an orbital medial wall defect with medial rectus injury and he underwent orbitotomy. Medial rectus innervation returned at postoperative 8 months. Several extraocular muscles may be traumatized during FESS. Timing and method of treatment are based on the severity and type of injury and the number of muscles involved. Treatment strategies are dependent on accurate interpretation of magnetic resonance imaging scans.