Background: Details and effects of individualised homeopathic treatment of headache (ICD-9: 784.0) in usual care have not yet been investigated. Methods: Prospective multi-centre observational study. Consecutive primary-care patients beginning homeopathic treatment were followed for 2 years, keeping regular records of complaint severity, health-related quality of life (QoL), and medication use. Results: 230 adults (77.0% women), age 38.2 ± 11.3 years, and 74 children (10.4 ± 3.2 years, 55.4% girls) treated by 73 physicians were included. Patients suffered from headaches (average duration: adults 9.3 ± 9.5 years, children 2.7 ± 2.6 years) and other chronic diseases. Most patients (adults 90.0%, children 70.8%) had been pre-treated (usually with conventional treatment). Severity of diagnoses and complaints showed marked improvements in the first 3 months, continuing on until the end of the study. For headache, standardised effects (mean change divided by standard deviation at baseline) in adults reached 1.63 (95% CI 1.78–1.49), 2.27 (2.45–2.09), and 2.44 (2.63–2.25) at 3, 12, and 24 months, respectively. In children, the standardised effects at these time points were 1.67 (1.91–1.44), 2.55 (2.82–2.28), and 2.74 (3.03–2.46), respectively. Whilst the QoL among adults improved over time, this trend was not observed in children. Use of conventional treatment and health services decreased markedly. Conclusion: This observational study of patients seeking homeopathic treatment because of headache showed consistent improvements over the 24-month period. The observational and uncontrolled character of the study design does not allow conclusions on a specific relationship between treatment and the observed effects.