Background: Intraosseous anesthesia is the process by which an anesthetic solution, after penetration of the cortical bone, is directly injected into the spongiosa of the alveolar bone supporting the tooth. This study aimed to compare the effectiveness of the traditional inferior alveolar nerve block (IANB) and computerized intraosseous anesthesia in the surgical extraction of impacted lower third molars, compare their side effects systemically by monitoring heart rate, and assess patients’ a posteriori preference of one technique over the other. Methods: Thirty-nine patients with bilaterally impacted third molars participated in this study. Each patient in the sample was both a case and control, where the conventional technique was randomly assigned to one side (group 1) and the alternative method to the contralateral side (group 2). Results: The traditional technique was faster in execution than anesthesia delivered via electronic syringe, which took 3 min to be administered. However, it was necessary to wait for an average of 6 ± 4 min from the execution to achieve the onset of IANB, while the latency of intraosseous anesthesia was zero. Vincent's sign and lingual nerve anesthesia occurred in 100% of cases in group 1. In group 2, Vincent’s sign was recorded in 13% of cases and lingual anesthesia in four cases. The average duration of the perceived anesthetic effect was 192 ± 68 min in group 1 and 127 ± 75 min in group 2 (P < 0.001). The difference between the heart rate of group 1 and group 2 was statistically significant. During infiltration in group 1, heartbeat frequency increased by 5 ± 13 beats per minute, while in group 2, it increased by 22 ± 10 beats per minute (P < 0.001).No postoperative complications were reported for either technique. Patients showed a preference of 67% for the alternative technique and 20% for the traditional, and 13% of patients were indifferent. Conclusion The results identified intraosseous anesthesia as a valid alternative to conventional anesthesia in impacted lower third molar extraction.