We aimed to disentangle the proportional contributions of upper and lower motor neuron dysfunction to motor impairment in children with spina bifida. We enrolled 42 children (mean age, 11.2 years; standard deviation, 2.8 years) with spina bifida and 36 control children (mean age, 11.4 years; standard deviation, 2.6 years). Motor impairment was graded to severity scales in children with spina bifida. We recorded motor evoked potentials after transcranial and lumbosacral magnetic stimulation and compound muscle action potentials after electric nerve stimulation. Regarding lower motor neuron function, severely impaired children with spina bifida demonstrated smaller compound muscle action potential areas and lumbosacral motor evoked potential areas than control children; mildly impaired children hardly differed from control children. Compound muscle action potential latencies and lumbosacral motor evoked potential latencies did not differ between children with spina bifida and control children. Regarding upper motor neuron function, children with spina bifida demonstrated smaller transcranial motor evoked potential areas and longer central motor conduction times than control children. The smallest motor evoked potential areas and longest central motor conduction times were observed in severely impaired children. In children with spina bifida, the contribution of upper motor neuron dysfunction to motor impairment is more considerable than expected from clinical neurologic examination.