General practitioners (GPs) diagnose and treat headache in primary care settings. The objective of this study was to investigate the effect of a 2-day headache education programme for GPs primarily on diagnostic accuracy. The education programme included theoretical lectures and face-to-face patient evaluation with headache specialists. Three GPs evaluated headache patients before and after the programme. Each GP was planned to interview a total of 60 patients (30 before, 30 after the programme). All patients were evaluated by headache specialists following evaluation by the GPs. A total of 189 patients were included in this study. Diagnostic accuracy increased from 56.3% to 81.0% after the headache education programme (P < 0.001), which also significantly improved the choice of proper treatment (P = 0.043). The headache education programme for GPs significantly improved diagnostic accuracy in patients with tension-type headache and the choice of proper treatment. Such education programmes can be standardized and given to GPs working in the primary care setting. These programmes can be arranged locally by the universities and might have a favourable impact on the diagnosis and treatment of headache.