Introduction: Diagnosis of emergent intracranial lesions that require emergency treatment either medically or surgically in non-traumatic pediatric headaches is important. Red-flag signs and symptoms are commonly used as justification for neuroimaging; however, evidence on its diagnostic values is limited. The study aims to identify diagnostic values of red-flags and develop a clinical prediction score to help improve the diagnostic yield of neuroimaging. Methods: A retrospective review of 109 pediatric patients from 2006 to 2020 who presented with a non-traumatic headache was conducted. A clinical prediction score from red flags was developed using multivariate logistic regression. Discriminatory ability was examined using the area under the receiver operating characteristic curve. Results: A total of 51 patients were diagnosed with emergent intracranial lesions. Four potential clinical red flag predictors were identified: (1) acute onset (less than 3 months), (2) altered conscious state, (3) focal motor abnormality, and (4) and ocular/pupillary abnormality or squint. A clinical prediction score was developed with good discriminatory properties (0.84). Conclusions: Clinical predictor scores from these four red flags may play an important role in maximizing neuroimaging and proper management for pediatric patients with non-traumatic headaches. Future validation studies are needed and could guide referrals and optimize the use of neuroimaging for these patients.