Background: This study analysed whether vertical measurements in the maxillary posterior region are more accurate using panoramic radiography (PAN) or cone-beam computed tomography (CBCT). Methods: Corresponding maxillary posterior regions on both PAN and CBCT images were selected and examined for vertical measurements. The vertical distance between the bone crest and the floor of the maxillary sinus was measured. Measurements in edentulous regions were performed using a similar procedure. Additionally, the vertical height of any defect, if present, was measured. Results were evaluated statistically. Results: When comparing corresponding regions on the CBCT and PAN images, 204 patients with a total of 341 measurements (n = 341) met the inclusion criteria. The mean values for all measurements were 7.21 ± 3.74 mm on PAN and 7.62 ± 4.06 mm on CBCT. The mean difference between all paired measurements was −0.41 ± 1.03 mm. Significant differences between PAN and CBCT were observed (p < 0.001). Defects were detected in 58 (17%) of the 341 measurements. The mean defect height was 1.85 ± 1.05 mm on PAN and 1.99 ± 1.00 mm on CBCT. No significant differences were noted between PAN and CBCT (p = 0.052). Conclusions: Although the relationship between vertical height measurements on PAN and CBCT showed a significant difference of −0.41 ± 1.03 mm for all paired measurements, the difference was very small upon closer inspection. Both PAN and CBCT are suitable methods for measuring vertical heights in the posterior maxilla.