The aim of this study was to evaluate the effects of intrusion of the maxillary posterior teeth with zygomatic anchorage on the dentofacial system, on electromyographic (EMG) activity of the masticatory muscles, and on vibration of the temporomandibular joint. The study sample consisted of 19 subjects (13 females, 6 males) with a mean age of 17.7 years. Lateral cephalometric and posteroanterior (PA) radiographs, EMG, and electrovibratographic (EVG) records were obtained before (T0) and after (T1) intrusion. Paired t- and Wilcoxon signed ranks tests were used for statistical evaluation. Maxillary molar intrusion of 3.37 ± 1.21 mm was obtained with a force of 400 g in an average period of 6.84 ± 1.64 months. At T1, all measurements showed that facial growth direction, ANB angle, convexity, and overjet were decreased (P < 0.05). SNB angle, facial depth, and overbite were significantly increased (P < 0.05). Upper lip-E plane distance was increased (P < 0.05). Evaluation of the PA radiographs showed that the right and left molar reference angles were unchanged. EMG and EVG analysis showed that the stomatognathic system at T0 was maintained at T1. Intrusion of the maxillary posterior teeth with zygomatic anchorage is an effective treatment alternative for anterior open bite correction.