A full-term female baby was diagnosed as having Apert syndrome with craniosynostosis, hypertelorism, syndactyly, polydactyly, and cleft plate. At her first ophthalmic visit at 8 months old, she was noted to have bilateral exophthalmos with epiblepharon on her lower lids, exotropia, and right inferior oblique muscle overaction (IOOA) and manifested right dissociated vertical deviation (DVD). There was no keratopathy or optic neuropathy. Bilateral lateral rectus muscles and right inferior oblique muscle recession were performed with correction of bilateral epiblepharon at 1 year of age. Orthotropia was achieved postoperatively. However, recurrent exotropia with left inferior oblique muscle overaction and manifested left DVD developed 2 years later. We performed left medial rectus muscle resection and left inferior oblique muscle recession, and the patient maintained orthotropia. Her best-corrected visual acuity was 6/8.6 in the right eye and 6/7.5 in the left eye at the latest follow-up. Amblyopia, OD, was still noted. We report this case of Apert syndrome with exophthalmos, exotropia, and IOOA. The exophthalmos progressed as the patient grew, thus the strabismus pattern changed during follow-up. Frequent follow-up and titrated management may be needed for such case to ensure good binocular vision.