Background Migraine is a frequent headache disorder with high disease burden. The aims of this study were to determine the administrative prevalence and incidence of migraine in Germany; and to elucidate disease characteristics, prescription patterns and the patient journey through the German healthcare system. Methods In this retrospective, observational study, adult patients with migraine (International Classification of Diseases, 10th revision, German modification G43) were identified in the anonymised German Company Sickness Fund database (CSFD) from 2008 through 2016. The administrative prevalence and incidence of migraine were calculated for the total CSFD study population and extrapolated to the German Statutory Health Insurance (SHI) population. Migraine subtypes, concurrent diagnoses, prescription patterns and visited healthcare professional groups were analysed. Results A total of 243,471 patients with migraine were identified in the CSFD (2008–2016); 78.0% were female and 45.3% were aged 35–54 years. The administrative prevalence of migraine, extrapolated to the SHI population, ranged between 2.89% in 2008 and 3.98% in 2016; administrative incidence ranged from 0.587% in 2009 to 0.267% in 2016, and varied between 0.399% and 0.442% during 2011 to 2015. Overall, 29.1% of patients received at least one prescription for any preventive medication listed in the German guideline. Only 7.9% received the same preventive medication for more than 1 year, with 82.9% of these patients discontinuing the medication before study end. Regarding acute medications, 74.2% of prescriptions were for analgesics/non-steroidal anti-inflammatory drugs and 21.2% were for triptans. General practitioners most commonly diagnosed and treated migraine in the CSFD population. Patients with prescriptions for two or more different preventive therapy classes had higher use of acute and emergency medications, and visited healthcare professionals and hospitals more frequently than patients with no prescriptions or prescriptions for only one preventive therapy class. Conclusions The administrative prevalence of migraine in this claims database suggests many patients with migraine did not seek medical care. Of those who did, fewer than one-third received preventive medication, with most patients having been prescribed only one such medication and few having continued treatment beyond 1 year. These outcomes suggest there is scope for improvement in migraine management in Germany.