Measuring pilot mental workload (MWL) is crucial for enhancing aviation safety. However, MWL is a multi-dimensional construct that could be affected by multiple factors. Particularly, in the context of a more automated cockpit setting, the traditional methods of assessing pilot MWL may face challenges. Heart rate variability (HRV) has emerged as a potential tool for detecting pilot MWL during real-flight operations. This review aims to investigate the relationship between HRV and pilot MWL and to assess the performance of machine-learning-based MWL detection systems using HRV parameters. A total of 29 relevant papers were extracted from three databases for review based on rigorous eligibility criteria. We observed significant variability across the reviewed studies, including study designs and measurement methods, as well as machine-learning techniques. Inconsistent results were observed regarding the differences in HRV measures between pilots under varying levels of MWL. Furthermore, for studies that developed HRV-based MWL detection systems, we examined the diverse model settings and discovered that several advanced techniques could be used to address specific challenges. This review serves as a practical guide for researchers and practitioners who are interested in employing HRV indicators for evaluating MWL and wish to incorporate cutting-edge techniques into their MWL measurement approaches.