Objective: Evidence on prophylactic drugs for pediatric migraine is limited, especially when comorbid conditions contribute to treatment resistance. This study evaluated the efficacy of cyproheptadine in children with migraine and explored the impact of comorbid neurodevelopmental disorders and orthostatic intolerance (OI). Methods: We retrospectively analyzed pediatric migraine patients treated with cyproheptadine. Efficacy was assessed based on the reduction in headache frequency, with responders defined as patients experiencing at least a 50% reduction in headache episodes. Fisher’s exact test analyzed the relationship between efficacy and comorbid conditions or treatment sequence. Multiple logistic regression was performed to identify factors associated with adverse events. Results: In total, 155 children (71 males, 84 females) aged 3–15 years were included. Comorbid neurodevelopmental disorders and OI were present in 27 (17.4%) and 22 (14.2%) patients, respectively. Efficacy was evaluated in 148 patients, with 68.9% classified as responders. Patients with comorbid conditions showed lower efficacy. Responders required a lower dose of cyproheptadine (p = 0.039). Multiple logistic regression identified headache frequency, cyproheptadine dose, and comorbid OI and neurodevelopmental disorders as factors influencing treatment efficacy. Conclusions: Cyproheptadine is effective in treating pediatric migraine, though patients with neurodevelopmental disorders and OI demonstrated reduced efficacy.
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