Purpose The purpose of this study is to describe the clinical characteristics and treatment results of medial rectus muscle (MR) transection incurred during endoscopic sinus surgery. Methods This retrospective study included 16 patients with MR transection incurred during endoscopic sinus surgery between 1994 and 2015. The operative notes of the surgical procedure, the pattern of strabismus, the type of muscle injury, the type of corrective strabismus surgery, and the surgical outcomes were reviewed. Results Nine patients had partial resection of MR and seven patients had complete transection of MR, resulting from an injury incurred during endoscopic sinus surgery. Three of the nine patients with partial resection injury were initially diagnosed as complete resection and subsequently rediagnosed as partial resection in a review of the images during this study. Five of the nine patients with partial MR resection underwent only simple recession/resection surgery. Patients with complete MR transection underwent muscle transposition or globe fixation surgeries and often multiple operations were required. Conclusions The results of this study showed that the treatment strategies could vary depending on the nature of muscle injury. In cases with complete transection, muscle transposition or globe fixation surgeries are often required, with multiple operations. However, partial muscle resection with only simple recession/resection surgery shows a favorable outcome in many cases. The use of proper imaging techniques, a thorough review of the images with various planes, and close follow-up are important for determining the nature of the muscle injury.