Aim To investigate the influence of clinical and demographic features on diagnostic delay in cluster headache patients, in order to discuss diagnostic pitfalls and raise disease awareness. Methods A large, well-characterized cohort of 400 validated cluster headache patients from the Danish Cluster Headache Survey, diagnosed according to ICHD-II, were investigated. ANOVA was applied to investigate differences in diagnostic delay between groups. Selected independent variables were assessed in relation to diagnostic delay using a gamma regression model. Results Diagnostic delay was significantly reduced for each decade of cluster headache onset from 1950–2010 ( p < 0.001). Onset after 1990 was associated with shorter diagnostic delay (OR = 0.28, p < 0.001), whereas attack duration > 180 minutes (OR = 1.62, p < 0.034), migraine-like features (OR = 1.30, p < 0.043) and nocturnal attacks (OR = 1.39, p < 0.021) were associated with prolonged diagnostic delay. Further, diagnostic delay decreased with age of onset (age < 20: 13.8 years, age 20–40: 5.4 years and age > 40: 2.1 years, p < 0.001). Conclusion Diagnostic delay was reduced for every decade investigated, whereas some atypical cluster headache features were associated with prolonged diagnostic delay. Better medical education and more disease awareness are needed to prevent misdiagnosis and prolonged diagnostic delay.