Root canal transportation is a significant concern in endodontic therapy, impacting treatment outcomes. ProTaper Next (PTN) and WaveOne Gold (WOG) are popular endodontic instrumentation systems used to shape root canals. This systematic review aimed to evaluate the literature on root canal transport with PTN and WOG. Fourteen studies were analyzed, highlighting the overall effectiveness of both systems. The PTN showed potential advantages in minimizing canal transport, while the WOG preserved the original canal shape. Operator experience and canal curvature influence performance. This review provides evidence-based insights to aid endodontic practitioners in making informed decisions for successful root canal treatments. The aim of this systematic review was to evaluate and synthesize the literature on root canal transportation with ProTaper Next (PTN) and WaveOne Gold (WOG) instrumentation systems in endodontic therapy. A comprehensive literature search was conducted using the PubMed Central, Scopus, EBSCO, Embase and Web of Science databases from 2000 to 2022. Studies that met the predefined inclusion and exclusion criteria were selected for analysis. Data on study design, participant characteristics, intervention details, comparison groups, outcomes, and results were extracted from the included studies. The methodological quality of the studies was assessed using appropriate tools, and the findings were synthesized qualitatively. A total of 14 studies were included in the systematic review. The analysis revealed that both the PTN and WOG systems demonstrated overall effectiveness in root canal preparation. PTN rotary files performed adequately with inexperienced operators and showed potential advantages in minimizing canal transportation. On the other hand, WOG files exhibited a conservative approach, preserving the original canal shape. However, variations in performance were observed depending on the instrumentation method, operator experience, and canal curvature. This systematic review provides valuable insights into the ability of the PTN and WOG to manage root canal transport. Both systems demonstrated satisfactory outcomes, with WOG often preserving the natural canal anatomy. The findings suggest that proper operator training and technique play vital roles in achieving optimal results. Clinicians should consider the unique characteristics of each system when selecting instrumentation for root canal treatments. Nonetheless, it is crucial to acknowledge the limitations of the included studies, such as variations in sample sizes and operator experience, which may impact the interpretability of the findings. Future research should address these limitations and further explore the efficacy of these instrumentation systems in various clinical settings. The evidence derived from this systematic review can aid endodontic practitioners in making evidence-based decisions for successful root canal procedures.