To examine factors for adherent and non-adherent behavior in patients with cluster headache and migraine. Adults with cluster headache or migraine were included in this anonymous online survey using a questionnaire accessed via homepages of headache support groups. Medication adherence in preventive treatment was measured with the Medication Adherence Report Scale (MARS-D). Factors for non-adherent behavior were examined (subjective socioeconomic status, psychological comorbidities, self-efficacy, coping, side effects, expectations of treatment, information on medical treatment, and trust in the physician/treatment concept). 200 participants (n = 58 with cluster headache, n = 142 with migraine) were included. The rate of medication adherence in preventive treatment was 32.8% for participants with cluster headache and 20.4% for migraine. The most common reasons for low adherence in participants with cluster headache were altering the prescribed medication dose (34%) or taking less than instructed (14%), which was mostly due to insufficient benefit from the medication or side effects. Positive expectations of medical treatment (p ≤ 0.05) correlated significantly with adherent behavior in cluster headache. Furthermore, the adherence-promoting factors coping and self-efficacy were more pronounced in patients with cluster headache than in those with migraine (p < 0.05). This study is the first to comprehensively investigate medication adherence and factors influencing adherent/non-adherent behavior in patients with cluster headache. Patients with cluster headache had similar adherence levels to patients with migraine, but had higher resources of adherence-promoting factors.