Introduction: Primary headaches impact substantially on daily activities of the sufferers leading to increased direct and indirect medical burden on its sufferers. It is a growing public health problem affecting an estimated 5.6% of Africans yet, among young Nigerians the disorder remains underestimated in scope and scale, under-recognized and under-treated. Methods: This was a questionnaire bases cross sectional study conducted in Enugu South East Nigeria. Frequency of headache and pain intensity were accessed questions (a) and (b) of the MIDAS questionnaire. Precipitating factors, drugs used, medical consultation and academic limitation were also assessed. Results: A total of 218 students were interviewed. The lifetime prevalence of primary headache was 74.3%. The corresponding prevalence of migraine and tension type headache were 7.8% and 32.6% respectively. Unlike migraine, tension type headache was significantly higher in females. Most headaches lasted 1-5 days (all primary headaches 24.7%, migraine 11.8% and TTH, 35.2%) similar in males and females. The proportion of students who worried over headache and attacks compared to those who did not: all primary headaches, 22.2%, who consulted a physician 16% and whose academic performance were often affected 26.5%. Limitation in academic performance was significantly higher among students that received medical consultation and students who worried over attacks. Conclusion: Primary headaches are common among secondary school children in Enugu, South East Nigeria, Nigeria. Most headaches last 1-5 days, frequently limit the academic activities of its sufferers and are sources of concern to the sufferers.