Background: Injuries to the lingual and inferior alveolar nerves (IAN) through third molar surgery are common and complicated clinical problems. Juxta-apical radiolucency (JAR) is one of the new radiographic signs, suggestive of IAN damage. Objectives: This study aimed to assess the relationship between JAR and IAN and to determine its effects on the cortical plate. Methods: In this cross-sectional study, after evaluating an initial sample of 450 cases, the cone-beam computed tomography (CBCT) images of 20 patients with JAR were compared with those of 20 age-matched patients without JAR in the axial and multi-planar images. The relationship between JAR and IAN was evaluated, and thinning of the mandibular cortical plates was also investigated. Statistical analysis was performed using descriptive tests and chi-square test in SPSS version 23. Results: The relationship between JAR and IAN was statistically significant (P = 0.001). The cortical plates were perforated in 75% of cases with JAR as opposed to 45% of cases without JAR (P = 0.06). The relationship between the location of JAR and IAN was also significant (P = 0.004). Conclusions: Based on the present results, JAR was associated with IAN in most cases. Thinning of the cortical plates was observed in all cases of JAR.