This systematic review evaluated how CBCT impacts diagnosis, treatment planning (TP) and confidence in endodontic cases compared to intraoral radiography (IR). PubMed/MEDLINE, Cochrane-CENTRAL, Embase, Scopus, LILACS, Web of Science and Google Scholar databases were searched. Information regarding changes in the diagnosis, TP and confidence after CBCT was evaluated. The methodological quality was assessed using QUADAS-2. Twenty-six studies were included, 10 classified as having a low risk of bias. Most studies focused on changes in TP (n = 10) or diagnosis in primary treatments (n = 7). Studies evaluating dental trauma showed the most significant improvement. CBCT impacted TP, increasing difficulty in choosing treatment for complex cases (external root resorption and complex root canal morphology) and often resulting in a more invasive treatment (i.e., tooth extraction). CBCT impacts diagnosis, TP and confidence in cases of complex endodontic treatments, often leading to more invasive treatments.