Craniosynostosis is the premature fusion of one or more sutures across the calvaria, resulting in morphological and health complications that require invasive corrective surgery. Finite element (FE) method is a powerful tool that can aid with preoperative planning and post-operative predictions of craniosynostosis outcomes. However, input factors can influence the prediction of skull growth and the pressure on the growing brain using this approach. Therefore, the aim of this study was to carry out a series of sensitivity studies to understand the effect of various input parameters on predicting the skull morphology of a sagittal synostosis patient post-operatively. Preoperative CT images of a 4-month old patient were used to develop a 3D model of the skull, in which calvarial bones, sutures, cerebrospinal fluid (CSF), and brain were segmented. Calvarial reconstructive surgery was virtually modeled and two intracranial content scenarios labeled “CSF present” and “CSF absent,” were then developed. FE method was used to predict the calvarial morphology up to 76 months of age with intracranial volume-bone contact parameters being established across the models. Sensitivity tests with regards to the choice of material properties, methods of simulating bone formation and the rate of bone formation across the sutures were undertaken. Results were compared to the in vivo data from the same patient. Sensitivity tests to the choice of various material properties highlighted that the defined elastic modulus for the craniotomies appears to have the greatest influence on the predicted overall skull morphology. The bone formation modeling approach across the sutures/craniotomies had a considerable impact on the level of contact pressure across the brain with minimum impact on the overall predicated morphology of the skull. Including the effect of CSF (based on the approach adopted here) displayed only a slight reduction in brain pressure outcomes. The sensitivity tests performed in this study set the foundation for future comparative studies using FE method to compare outcomes of different reconstruction techniques for the management of craniosynostosis.