Implant surgery in individuals with atrophic maxilla presents challenges, particularly concerning nasal cavity complications such as perforations, implant migration, and airway obstruction. While panoramic radiographs offer diagnostic convenience, their two-dimensional nature limits the evaluation of anatomical structures. Cone beam computed tomography (CBCT) provides a three-dimensional assessment, enhancing surgical planning accuracy and potentially reducing complications. With the aim of understanding the measurement differences between panoramic radiographs and CBCT images, this retrospective study examined CBCT images of patients with severely atrophic maxilla taken between September 2021 and December 2023 at the Ahmet Keleşoğlu Faculty of Dentistry. Virtual implants were placed in various tooth regions using OnDemand3D software. The incidence of nasal cavity perforations and vertical bone height differences between panoramic radiographs and CBCT images were evaluated. For this purpose, vertical bone length measurements in panoramic and CBCT images were compared for the virtual implant placement areas. Statistical analyses, including t-tests and ANOVA, were performed to determine significant differences among quantitative measurements, and a chi square test with Bonferroni corrected z-tests were used for possible associations between ratios. CBCT data from 59 patients, totaling 1888 virtual implants, revealed significant differences in implant depths among tooth regions (F = 9.880, p < 0.001). Canine regions showed higher perforation risks, especially with 12 mm and 14 mm implants. Panoramic radiographs often overestimated vertical bone height in canine and first premolar regions compared to CBCT measurements, which could lead to increased perforation risks. Radiographic evaluations using CBCT prior to implant surgery in atrophic maxilla cases are crucial to prevent nasal cavity complications. Panoramic radiographs may inadequately represent three-dimensional anatomy, underscoring the importance of CBCT for accurate implant placement and surgical planning. Further studies should consider varying implant sizes and brands to generalize findings.