Objective This study aimed to evaluate the condylar positional changes following mandibular reconstruction with preservation of the condylar head using Cone-Beam Computed Tomography (CBCT). Also, to assess joint space changes and the overall volumetric space compared to the preoperative status. Methodology This prospective study included 30 patients (60 joints) subjected to unilateral mandibular resection and reconstruction with preservation of the condylar head. The Helkimo index and preoperative (T1), two weeks postoperative (T2), and follow-up CBCTs (T3) after at least six months were gathered and processed to evaluate the condylar position and TMJ joint space using Anatomage Invivo 6. A student’s t-test and repeated-measures ANOVA statistics were used. A P value of less than 0.05 was considered statistically significant. Results Thirty patients (14 males, 16 females) with a mean age of 40.01 ± 12.7 years (a range of 18.1–62.9 years) were included. On the tumor side, there were significant variances in the vertical and mediolateral condylar positions between the three-time points (T1, T2, T3). Immediately after the operation, the condyles were significantly displaced in a downward direction at T2, which became larger after the last follow-up period (T3) (p = 0.007). The condylar positions at the anteroposterior direction were relatively stable without significant differences between the three times points (p = 0.915). On the non-tumor side, the condylar positions were relatively stable in the mediolateral and anteroposterior positions. In the tumor side, all of the TMJ spaces were significantly increased in size following the mandibular reconstructions (T2 and T3). However, on the non-tumor side, the anterior, posterior, and medial joint spaces were significantly changed postoperatively. Conclusion After mandibular reconstruction with condylar preservation, the condylar position and volumetric measurement immediately changed noticeably and continued to be a permanent change over time compared to relatively stable condyles on the non-tumor side. According to Helkimo index, patients become adapted to the postoperative changes without significant differences between the two sides.