Synesthesia is a neurological condition in which an inducer stimulus in one sense leads to a concurrent percept in a second sense. The immune hypothesis of synesthesia links synesthesia to immune-related conditions such as migraine. More specifically, migraine with aura may be linked to grapheme-color synesthesia as both involve cortical hyperexcitability. In this study, 161 female synesthetes, and 92 female nonsynesthetes, completed an online questionnaire about synesthesia and migraine. We found no general link between migraine and synesthesia nor between migraine with aura and grapheme-color synesthesia. Exploratory analyses, however, showed that certain types of synesthetic inducer (non-linguistic visual experiences, scent, taste, emotion and personality) were associated with visual disturbances in headache among female participants, and touch as a concurrent was associated with migraine with aura. On the basis of our exploratory analyses, we hypothesize that specific subtypes of synesthesia are related to migraine. The relationship between these two conditions is likely to become clearer as research on the underlying causes of synesthesia and migraine progresses.