Objective To investigate the frequency, attack characteristics, and treatment experiences of migraine and tension-type headache (TTH) among gender dysphoric female-to-male (FtM) participants as well as in relation to psychiatric comorbidities and real-life experience that relates to being transgender in Turkey. Background There are only a few publications to date on transgender individuals with headache. Further studies to understand the distinctive needs might provide better management. Methods A total of 88 gender dysphoric FtM individuals (mean (SD) age: 24.8 (5.7) years) were included on a voluntary basis in this cross-sectional survey. Each participant filled out the questionnaire form that elicited items on sociodemographic characteristics, Gender Identity Transition Inventory, Beck Depression Inventory (BDI), Beck Anxiety Inventory (BAI), and Headache Questionnaire. Results Overall, 32/88 (36.4%; 95% confidence interval [CI]: 27.0%-47.0%) participants were diagnosed with migraine, and 36/88 (40.9%; 95% CI: 31.5%-52.3%) participants were diagnosed with TTH. High rates of unemployment, smoking, and social drinking were observed in our sample compared with the general population in Turkey. The three-item ID migraine screener was positive in 20.5% (18/88 patients) of our population. Patients with migraine in comparison with patients with TTH had statistically significantly higher BDI [12.0 (1-50) vs. 7.0 (0-33); p = 0.013] and BAI [13 (1-48) vs. 5 (0-22); p = 0.016] scores, longer headaches in the past month [median 3 vs. 1 day; p < 0.001], higher Numerical Rating Scale scores for headache severity [7 (2-10) vs. 5 (1-9), p < 0.001], and higher likelihood of menstruation acting as a triggering factor [8/32 patients (25.0%) vs. 0/36 patients (0.0%); p = 0.001] as well as increased rates of previously given diagnosis by a physician [15/32 patients (46.9%) vs. 4/36 patients (11.1%); p < 0.001], a greater number of neuroimaging tests being performed [12/32 patients (37.5%) vs. 3/36 patients (9.1%); p = 0.012], and a higher rate of emergency room utilization [7/32 patients (21.9%) vs. 1/36 patients (2.8%); p = 0.039] for headache. Conclusions In the FtM transgender population we investigated, migraine and TTH were quite common. The screening and early recognition of comorbid migraine, as well as the comorbid depression and anxiety, seem to be important in gender dysphoric FtM individuals. Further studies are needed to better understand the potential interaction of migraine with comorbid psychiatric disorders and the prevalence of headache types and gender-affirmative hormone treatment outcomes in the transgender population.