(1) Background: The aim of the study was to assess the potential effectiveness of clinical diagnostic examinations, such as muscle palpation, and instrumental examinations, such as electromyography, in the early detection of TMJ involvement in patients with juvenile idiopathic arthritis (JIA), as early diagnosis of these disorders can reduce the risk of developing facial growth anomalies and dento-skeletal malocclusions. (2) Methods: Evaluations were conducted on a cohort of 15 people with juvenile idiopathic arthritis (JIA) and a comparison group of 15 healthy participants at the start of the trial (T0) and after 18 ± 6 months (T1). Data were obtained through clinical examination, involving muscle palpation of the anterior temporalis, masseters, and sternocleidomastoids, and by instrumental analysis using electromyography. The parametric student’s t-test was used to evaluate group comparisons for data that were normally distributed, whereas the nonparametric Mann–Whitney U test was employed for parameters that did not follow a normal distribution. (3) Results: In the JIA group, higher levels of pain were recorded in the sternocleidomastoid muscles on both sides as compared to the control group (p < 0.05) at both T0 and T1. Electromyography revealed no statistically significant variances both in the JIA group and in the control group, except for the IMP index, characterized by a significant improvement over time for the JIA group. (4) Conclusions: According to the methodology employed in this study, all JIA patients had TMD symptoms, mainly muscle disorders. The existence of statistically significant parameters suggests the potential to regard muscle palpation and electromyography as predictive indicators of TMJ involvement in JIA subjects. Additional research is required to validate their reliability.