AIM: To evaluate the differences in the functional connectivity (FC) of the primary visual cortex (V1) between the youth comitant exotropia (CE) patients and health subjects using resting functional magnetic resonance imaging (fMRI) data. METHODS: Totally, 32 CEs (25 males and 7 females) and 32 healthy control subjects (HCs) (25 males and 7 females) were enrolled in the study and underwent the MRI scanning. Two-sample t-test was used to examine differences in FC maps between the CE patients and HCs. RESULTS: The CE patients showed significantly less FC between the left brodmann area (BA17) and left lingual gyrus/cerebellum posterior lobe, right middle occipital gyrus, left precentral gyrus/postcentral gyrus and right inferior parietal lobule/postcentral gyrus. Meanwhile, CE patients showed significantly less FC between right BA17 and right middle occipital gyrus (BA19, 37). CONCLUSION: Our findings show that CE involves abnormal FC in primary visual cortex in many regions, which may underlie the pathologic mechanism of impaired fusion and stereoscopic vision in CEs.