This study used ultrasonography to compare the thickness and cross-sectional area of the masticatory muscles in patients with temporomandibular joint arthralgia and investigated the differences according to sex and the co-occurrence of headache attributed to temporomandibular disorders (HATMD). The observational study comprised 100 consecutive patients with TMJ arthralgia (71 females and 29 males; mean age, 40.01 ± 17.67 years) divided into two groups: Group 1, including 86 patients with arthralgia alone (60 females; 41.15 ± 17.65 years); and Group 2, including 14 patients with concurrent arthralgia and HATMD (11 females; 33.00 ± 16.72 years). The diagnosis of TMJ arthralgia was based on the diagnostic criteria for temporomandibular disorders. The parameters of the masticatory muscles examined by ultrasonography were subjected to statistical analysis. The pain area (2.23 ± 1.75 vs. 5.79 ± 2.39, p-value = 0.002) and visual analog scale (VAS) score (3.41 ± 1.82 vs. 5.57 ± 12.14, p-value = 0.002) were significantly higher in Group 2 than in Group 1. Muscle thickness (12.58 ± 4.24 mm) and cross-sectional area (4.46 ± 2.57 cm²) were larger in the masseter muscle than in the other three masticatory muscles (p-value < 0.001). When examining sex-based differences, the thickness and area of the masseter and lower temporalis muscles were significantly larger in males (all p-value < 0.05). The area of the masseter muscle (4.67 ± 2.69 vs. 3.18 ± 0.92, p-value = 0.004) and lower temporalis muscle (3.76 ± 0.95 vs. 3.21 ± 1.02, p-value = 0.049) was significantly smaller in Group 2 than in Group 1. An increase in VAS was significantly negatively correlated with the thickness of the masseter (r = - 0.268) and lower temporalis (r = - 0.215), and the cross-sectional area of the masseter (r = - 0.329) and lower temporalis (r = - 0.293). The masseter and lower temporalis muscles were significantly thinner in females than in males, and their volumes were smaller in patients with TMJ arthralgia and HATMD than in those with TMJ arthralgia alone. HATMD and decreased masseter and lower temporalis muscle volume were associated with increased pain intensity.