Background Headache disorders are globally prevalent and insufficient treatment contribute to low quality of life, increased disability, and socioeconomic costs. However, headache can to a large extent be treated appropriately by general practitioners. Objective To explore general practitioners' (GPs') management of patients with headache lasting >= 6 months. Methods In this retrospective descriptive cross-sectional study based on medical audit, all GPs practicing in Vejle municipality (population 116,992), Denmark, were invited to review their latest 20 patients with headache. Outcome measures were headache diagnostics, treatment, and referrals. Factors associated with referral to neurological treatment were examined by logistic regression. Results Of 26 invited practices, 19 participated reporting on 367 patients with lasting headache (71.4% women; mean-age 48.5 years). One hundred and sixty-one patients had migraine (44%; IQR: 28-60%), 140 (38%; IQR: 25-44%) had tension-type headache; 243 (66%; IQR: 50-79%) used simple analgesics, 147 (40%; IQR: 29-59%) triptans, 37 (10%; IQR: 0-14%) opioids, 93 (25%; IQR: 20-35%) were prescribed preventive medication; 176 (48%; IQR: 48-59%) were referred to neurologist, and 92 (25%; IQR: 10-37%) were referred to CT or MRI scan. Associated factors for referral were >1 headache diagnosis (aOR 1.75 [95% CI: 1.05-2.95]; P = 0.03), post-traumatic headache (aOR 2.53 [95% CI: 1.25-5.38]; P = 0.01), unspecific headache (aOR 2.04 [95% CI: 1.08-3.93]; P = 0.03), and using preventive treatment (aOR 2.75 [95% CI: 1.68-4.57]; P < 0.001). Conclusion This study provides insights to how GPs manage patients with long-lasting headache. Focus should be on reducing opioids, increasing preventive treatment, and keeping more patients in primary care.