There are limited studies about the effects of occlusal appliance (OA) after three months of use. This study aimed to compare myofascial pain (MP) according to RDC/TMD, craniocervical relationships (CR) and masseter and temporalis bilateral electromyographic (EMG) activity, before and after three months of occlusal appliance use. Nineteen patients participated in this study. Cephalometric and RDC/TMD diagnostics were performed previously (baseline) and at the end of the study period (three months). EMG recordings at clinical mandibular rest position (MRP), during swallowing of saliva (SW) and during maximum voluntary clenching (MVC) were performed as follows: after one hour of use of an OA; after three months of using the OA for a minimum of 16 hours each day; and immediately after removal from the mouth. MP was relieved in all patients at the end of the study period. CR did not change significantly between baseline and after removal of the OA at the end of the study period. EMG activity during MRP, SW, and MVC decreased in both muscles after one hour using the OA and maintained the same level for the three-month period. When comparing baseline versus final EMG activity without OA, a significant decrease was only observed in the masseter muscle. The results observed in the present study are relevant to clinicians because they imply that the therapeutic effect of OA does not significantly affect the homeostasis of the craniocervical system.