Objectives The aim of this study was to address the diagnostic efficacy of cone beam computed tomographic (CBCT) imaging in periodontics based on a systematic search and analysis of the literature using the hierarchical efficacy model. Methods A systematic search of the electronic databases such as PubMed, Scopus, Web of Science, and Cochrane was conducted until February 2019 to identify studies addressing the efficacy of CBCT imaging in Periodontics. The identified studies were subjected to pre-identified inclusion criteria followed by an analysis using a hierarchical model of efficacy (model) designed for an appraisal of the literature on a diagnostic imaging modality. Two examiners performed the eligibility and quality assessment of relevant studies, and consensus was reached where disagreement was found. Results The search resulted in 64 studies. Of these, 35 publications were allocated to the relevant level of efficacy and quality assessments wherever applicable. The overall diagnostic accuracy studies showed the risk of bias and applicability concerns in the use of CBCT to be low to moderate. In addition, CBCT is accurate in identifying periodontal defects when compared to other modalities. The studies on the level of patient outcomes agreed that CBCT is a reliable tool for the assessment of the outcomes after the treatment of periodontal defects. Conclusion CBCT was found to be beneficial and accurate in cases of infra-bony defects and furcation involvements.