Introduction Trigeminal autonomic cephalalgias (TACs) are characterized by paroxysmal attacks of unilateral primary headaches associated with ipsilateral craniofacial autonomic symptoms. In this pediatric case series, 13 cases of short-lasting unilateral neuralgiform headache attacks with conjunctival injection and tearing (SUNCT)/short-lasting unilateral neuralgiform headache with autonomic symptoms (SUNA), including children ages 3–18 years, are discussed. This paper reviews the application of International Classification of Headache Disorders, 3rd edition (ICHD-3) criteria especially in children presenting with SUNCT or SUNA. This is the largest pediatric case series of SUNCT/SUNA reported in the literature. Background Trigeminal autonomic cephalalgias are rare in children and adolescents, with SUNCT/SUNA having the least reported cases. We will discuss the application of ICHD-3 criteria to diagnose SUNCT/SUNA in children and review overlapping cases and their response to different treatment options including indomethacin, which is typically reserved for specific subtypes of TACs; for example, paroxysmal hemicrania. Conclusion This case series presents a unique opportunity to aid in the diagnosis and treatment of similar pediatric cases in the future. It helps us to broaden the ICHD-3 criteria to diagnose and treat different overlapping trigeminal autonomic cephalalgia cases in children.