Myogenic temporomandibular disorders (TMDs) are commonly associated with pain sensitization (PS), manifesting decreased local and distal pressure pain thresholds (PPTs). Aerobic exercise (AE) has shown hypoalgesic effects on PS. This study aimed to analyze the effects of AE in addition to physical therapy (PT) on widespread PS in myogenic TMDs. A randomized controlled trial was carried out, involving 20 subjects allocated to PT (n = 10) or PT + AE (n = 10). Both groups performed six sessions over four weeks, consisting of education, manual therapy, and therapeutic exercise. The PT + AE group also performed high-intensity intervallic AE on a stationary bike. Primary outcome: PPT in the Achilles tendon assessed with an algometer. Secondary outcome: Central Sensitization Inventory (CSI). Outcomes were recorded at baseline (T0), post-intervention (T1), and after 12 weeks (T2). Significant between-groups differences were found favoring PT + AE at T1 and T2 for the left Achilles PPT (T1 p < 0.01; d = 1.3; T2 p < 0.001; d = 2.5) and CSI (T1 p < 0.001; d = 2.3; T2 p < 0.01; d = 1.7), and at T2 for the right Achilles PPT (p < 0.001; d = 0.9). Thus, adding AE to PT improved widespread PS more than only PT in myogenic TMD.