Background: This study aimed to assess the course of anxiety and pain during lower third molar (LTMo) surgery and explore the role of mobile and single-channel electroencephalography under clinical and surgical conditions. Methods: The State-Trait Anxiety Inventory (STAI), Corah’s Dental Anxiety Scale (DAS), and Interval Scale of Anxiety Response (ISAR) were used. The patient self-rated anxiety (PSA), the pain felt during and after surgery, EEG, heart rate (HR), and blood pressure (BP) were assessed. Results: The Attention (ATT) and Meditation (MED) algorithms and indicators evaluated in this study showed several associations. ATT showed interactions and an association with STAI-S, pain during surgery, PSA level, HR, and surgical duration. MED showed an interaction and association with DAS, STAI-S, and pain due to anesthesia. Preclinical anxiety parameters may influence clinical perceptions and biological parameters during LTMo surgeries. High STAI-Trait and PSA scores were associated with postoperative pain, whereas high STAI-State scores were associated with more pain during anesthesia and surgery, as well as DAS, which was also associated with patient interference during surgery due to anxiety. Conclusions The findings suggest that single-channel EEG is promising for evaluating brain responses associated with systemic reactions related to anxiety, surgical stress, and pain during oral surgery.