Congenital Muscular Torticollis (CMT) is a neuromuscular disease in children, which leads to exacerbation of postural deformity and neck muscle dysfunction with age. Towards facilitating functional assessment of neuromuscular disease in children, topographic electromyography (EMG) maps enabled by flexible and stretchable surface EMG (sEMG) electrode arrays are used to evaluate the neck myoelectric activities in this study. Customed flexible and stretchable sEMG electrode arrays with 84 electrodes were utilized to record sEMG in all subjects during neck motion tasks. Clinical parameter assessments including the cervical range of motion (ROM), sonograms of the sternocleidomastoid (SCM), and corresponding histological analysis were also performed to evaluate the CMT. The muscle activation patterns of neck myoelectric activities between the CMT patients and the healthy subjects were asymmetric during different neck motion tasks. The CMT patients presented significantly lower values in spatial features of two-dimensional (2D) correlation coefficient, left/right energy ratio, and left/right energy difference (p < 0.001). The 2D correlation coefficient of activation patterns of neck rotation and extension in CMT patients significantly correlated with clinical parameter assessments (p < 0.05). The findings suggest that the spatial features of muscle activation patterns based on the sEMG electrode arrays can be utilized to evaluate the CMT. The flexible and stretchable sEMG electrode array is promising to facilitate the functional evaluation and treatment strategies for children with neuromuscular disease.