Objective Neuroimaging in headache patients identifies clinically significant neurological abnormalities and plays an important role in excluding secondary headache diagnoses. We performed a systematic review and meta-analysis of the existing guidelines and studies surrounding neuroimaging in headache patients. Methods The research question involved determining the prevalence of detecting clinically significant neurological abnormalities using neuroimaging in patients suspected of primary headache. Searches of the PubMed and Embase databases were conducted on English- language studies published from 1991 to 2016, and the reference lists of the retrieved articles were also checked manually. All headache subtypes and patients aged ≥15 years were included in the analysis. Results Ten studies met the selection criteria. The pooled prevalence of detecting clinically significant abnormalities in the neuroimaging of headache patients was 8.86% (95% confidence interval: 5.12–15.33%). Subsequently, diverse subgroup analyses were performed based on the detection method, headache type, study type, study region, age group, and disease type. Conclusion The present findings indicate that limited neuroimaging methods should be carefully considered for headache diagnostic purposes when there are red flag symptoms. Limitations and suggested directions for future studies on neuroimaging in headache patients are described.