Abstract Objective To assess the effects of three 8-week exercise programs on the frequency, intensity, and impact of headaches in patients with headache attributed to temporomandibular disorder (TMD). Methodology Thirty-six patients diagnosed with headache attributed to TMD participated in the study and were divided into three groups of 12 patients: a therapeutic exercise program (G1, mean age: 26.3±5.6 years), a therapeutic and aerobic exercise program (G2, mean age: 26.0±4.6 years), and an aerobic exercise program (G3, 25.8±2.94 years). Headache frequency and intensity were evaluated using a headache diary, and the adverse headache impact was evaluated using the Headache Impact Test (HIT-6). The intensity was reported using the numerical pain rating scale. These parameters were evaluated twice at baseline (A01/A02), at the end of the 8-week intervention period (A1), and 8-12 weeks after the end of the intervention (A2). Results At A1, none of the G2 patients reported having headaches, in G1, only two patients reported headaches, and in G3, ten patients reported headache. The headache intensity scores (0.3 [95% CI: -0.401, 1.068]), (0.0 [95% CI: -0.734, 0.734]) and HIT-6 (50.7 [95% CI: 38.008, 63.459]), (49.5 [95% CI: 36.808, 62.259]), significantly decreased in G1 and G2 at A1. At A2 headache intensity scores (0.5 [95% CI: -0.256, 1.256]), (0.0 [95% CI: -0.756, 0.756]) and HIT-6 (55.1 [95% CI: 42.998, 67.268]), (51.7 [95% CI: 39.532, 63.802]) in G1 and G2 haven't change significantly. The effects obtained immediately after the completion of the intervention programs were maintained until the final follow-up in all groups. Conclusion The programs conducted by G1 (therapeutic exercises) and G2 (therapeutic and aerobic exercise) had significant results at A1 and A2.