Posterior fossa arachnoid cysts (PFAC) may produce not only neurological symptoms but also other symptoms still poorly understood such as behavioral and learning deficits, awkwardness, and difficulties in social interaction. These subtle social impairments have not been formally described and their underlying brain mechanisms remain unknown. In the present case-control study, we aimed to empirically characterize social impairments in a pediatric population with PFAC using eye tracking. In addition, we investigated putative functional cortical abnormalities in these children using arterial spin labeling magnetic resonance imaging. Overall, 15 patients with PFAC (3f, age = 9.4 ± 4 years) and 43 typically developing volunteer children (16f, age = 9.3 ± 3.6 years) were enrolled in this study. Eye tracking was used to record gaze patterns during visualization of social interaction scenes. Viewing times to faces of characters and non-social background were analyzed. A voxel-wise whole-brain analysis was performed to investigate rest cerebral blood flow (CBF) abnormalities. Significantly reduced viewing time to faces was observed in patients compared with controls (p < 0.01). A ROC curve analysis revealed that 30% of PFAC patients presented viewing time to the face lower than the cutoff, while none of the controls did. The whole-brain analysis revealed a significant decrease in rest CBF in PFAC patients compared with controls bilaterally in the superior temporal gyrus and the temporoparietal junction (TPJ) (p < 0.05 FWE). These results suggest that early life PFAC may have an impact on functional activity of the temporal lobe, which could be associated with social perception deficits.