A randomized controlled trial was performed to compare the short-term effectiveness of botulinum toxin injections and physiatric treatment provided by means of Fascial Manipulation techniques in the management of myofascial pain of jaw muscles. Thirty patients with a Research Diagnostic Criteria for Temporomandibular Disorders (RDC/TMD) diagnosis of myofascial pain were randomized to receive either single-session botulinum toxin injections (Group A) or multiple-session Fascial Manipulation (Group B). Maximum pain levels (VAS ratings) and jaw range of motion in millimeters (maximum mouth opening, protrusion, right and left laterotrusion) were assessed at baseline, at the end of treatment, and at a three-month follow-up. Both treatment protocols provided significant improvement over time for pain symptoms. The two treatments seem to be almost equally effective, Fascial Manipulation being slightly superior to reduce subjective pain perception, and botulinum toxin injections being slightly superior to increase jaw range of motion. Differences between the two treatment protocols as to changes in the outcome parameters at the three-months follow-up were not relevant clinically. Findings from the present investigation are in line with literature data supporting the effectiveness of a wide spectrum of conservative treatment approaches to myofascial pain of the jaw muscles. Future studies on larger samples over a longer follow-up span are needed on the way to identify tailored treatment strategies.