The neural tube abnormality known as split cord malformation (SCM) is characterized by longitudinally separated functional hemicords. SCM is the result of a single basic ontogenetic error and may be associated with other anomalies. One such anomaly is Klippel-Feil syndrome (KFS), which is characterized by abnormal fusion of two or more cervical vertebrae. We present the case of a 15-year-old boy with a history of mandibular deformity, neck pain, and stiffness. Diagnostic imaging revealed type II cervical SCM, KFS, C1 vertebral arch anomaly, thoracic syringomyelia, and S1 paraspinous cleft. He was treated symptomatically with ultrasound-guided intramuscular injection of botulinum toxin (BT). Follow-ups showed that the treatment had a good effect on pain and stiffness, and an improvement in head posture was also achieved. Seven months after the first injection, a second injection was performed because the effect of BT diminished. In this report, we present the first case of cervical SCM type II associated with KFS treated symptomatically with BT injection. This is also the first reported case in a male patient; only 10 cases with both anomalies have been published in PubMed, and all of these cases are in females.