Apert syndrome is characterized by eyelid dysmorphology, V-pattern strabismus, extraocular muscle excyclorotation, and elevated intracranial pressure (ICP). We compare eyelid characteristics, severity of V-pattern strabismus, rectus muscle excyclorotation, and ICP control in Apert syndrome patients initially treated by endoscopic strip craniectomy (ESC) at about 4 months of age versus fronto-orbital advancement (FOA) performed about 1 year of age. Twenty-five patients treated at Boston Children's Hospital met inclusion criteria for this retrospective cohort study. Primary outcomes were magnitude of palpebral fissure downslanting at 1, 3, and 5 years of age, severity of V-pattern strabismus, rectus muscle excyclorotation, and interventions to control ICP. Before craniofacial repair and through 1 year of age, none of the studied parameters differed for FOA versus ESC treated patients. Palpebral fissure downslanting became statistically greater for those treated by FOA by 3 ( < 0.001) and 5 years of age ( = 0.001). Likewise, severity of palpebral fissure downslanting correlated with severity of V-pattern strabismus at 3 ( = 0.004) and 5 ( = 0.002) years of age. Palpebral fissure downslanting and rectus muscle excyclorotation were typically coexistent ( = 0.053). Secondary interventions to control ICP were required in four of 14 patients treated by ESC (primarily FOA) and in two of 11 patients initially treated by FOA (primarily third ventriculostomy) ( = 0.661). Apert patients initially treated by ESC had less severe palpebral fissure downslanting and V-pattern strabismus, normalizing their appearance. Thirty percent initially treated by ESC required secondary FOA to control ICP.