Background: Cranial surface electromyography is assumed to analyze the correlation between the stomatognathic apparatus and the muscular system and its implications on the physical status of professional athletes. The purpose of this paper is to evaluate surface cranial electromyography as an aid in the diagnosis and treatment of occlusal and muscular disorders in professional athletes. Methods: A sample of 25 athletes (mean age 23 years, 20 men and 5 women) underwent electromyographic recording; among them, 13 had a sports injury condition (symptomatic athletes), while 12 were in perfect physical condition (asymptomatic athletes). At odontostomatological examination, 6 showed cranio-mandibular disorders (dysfunctional athletes), while 19 showed no disorders (functional athletes). The treatment plan to resolve the symptoms of the dysfunctional athletes was chosen based on the electromyographic data. One month after the start of therapy with an occlusal splint, a follow-up was performed, and the results were compared with the initial data. Results: Statistical analysis showed that the chosen therapy following the use of electromyography was effective in 72% of cases, while 28% of patients did not respond to therapy (p = 0.028). Conclusions: The use of cranial electromyography in competitive athletes is a valuable tool in therapeutic choice aimed at balancing occlusal loads and improving the patient’s global tonic postural attitude, resulting in positive feedback in the qualitative assessment of sports performance.