Purpose: Unicoronal synostosis (UCS) has been associated with reading, language, and social dysfunction. Limited brain function connectivity studies exist for UCS with none devoted to comparing outcomes by side of synostosis (left versus right-sided UCS). Methods: Twelve patients with surgically treated UCS, 7 rightsided and 5 left-sided, were age matched to healthy controls. Resting state functional MRI was acquired in a 3T Siemens TIM Trio scanner (Erlangen, Germany). Data was collected with intrinsic connectivity distribution and seed-connectivity analysis using BioImage Suite (Yale School of Medicine). Region of interest analysis was performed based on Brodmann areas related to emotional, executive, language, motor, and visuo-spatial function. Significance was set at P < 0.05. Results: Compared to controls, all UCS patients demonstrated decreased connectivity in areas of the parietal and temporal cortices responsible for visuo-motor coordination and language function. Right UCS patients demonstrated decreased intrinsic connectivity in regions related to complex motor movement and proprioception relative to control subjects. Left UCS patients demonstrated decreased seed connectivity between regions of the parietal lobe and occipital lobe related to motor coordination, visual function, and language compared to right UCS patients. Conclusion: Unicoronal synostosis had decreased functional connectivity in regions associated with memory, visual information processing, and motor function. Moreover, left-sided UCS had decreased connectivity in circuits for motor coordination and language when compared to right-sided UCS. This study provides data suggestive of long-term sequelae of UCS that varies by sidedness, which may be responsible for neurocognitive impairments found in previous cognitive analyses.