Aim: This study sought to develop a process and methodology that could be a useful clinical and research tool for successfully completing functional magnetic resonance imaging (fMRI) scanning in children with Cerebral Palsy. Method: Six children with CP (mean age of 8.83 years; five with spastic hemiplegia, one with spastic quadriplegia) and three children with typical development (mean age of 9.33 years) completed an fMRI scanning protocol that used real-time motion feedback as a means of minimizing head and trunk motion. Anatomical, resting-state, and motor-task scans were sequentially obtained from each subject. Precentral “hand-knob” regions were identified on the anatomical scan and served as seed regions to reveal the functional connectivity of each subject’s brain as associated with hand movement. Results: Real-time motion feedback aided children in successful completion of resting state scans. Functional connectivity and brain activity mapping were obtained based on anatomical landmarks, and laterality indices were developed based on the obtained functional-connectivity map to specify a dominant side of brain activity that was matched to a clinical profile, despite anatomical variations that occur with Cerebral Palsy. Interpretation: Real-time motion feedback and the development of laterality indices can improve the clinical and research utility of fMRI scanning. What this paper adds: 1)Presents a real-time imaging protocol for fMRI to help children complete scanning; 2) Presents an fMRI methodology to obtain laterality indices in the presence of abnormal anatomy; 3) Provides findings of LI that match clinical diagnosis.