The functional resonance analysis method (FRAM) is a system-based method to understand highly complex sociotechnical systems. Besides learning from safety occurrences or undesirable states, FRAM can be used to understand how things go well in a system, by identifying gaps between “work as imagined” (WAI) and “work as done” (WAD). FRAM is increasingly used in many domains and can enhance our understanding of a complex system and proposes strategies to refine the work design. This systematic review identified 108 FRAM research papers from 2006–2019. Most of these papers were conducted by European researchers and employed qualitative methods such as document analysis, interviews, and focus groups with subject matter experts (SMEs) and observations to develop WAI and WAD. Despite being used in healthcare, construction, and maritime sectors among others, aviation was the most commonly explored domain in FRAM studies. The 26 FRAM studies in aviation explored many aspects of the aviation industry, including Air Traffic Control (ATC) systems, cockpit operation, ground handling, maintenance, and a range of past safety incidents, like runway incursions. This paper also characterises the FRAM studies focused on aviation in terms of the common methods and steps used to build FRAM and the available software tools to build FRAM nets. Current FRAM illustrates its advantages in capturing the dynamic and nonlinear nature of complex systems and facilitates our understanding and continual improvement of complex systems. However, there are some critical issues in FRAM use and interpretation, such as the consistency of methods and complexity and reliability of data collection methods, which should be considered by researchers and FRAM users in industry.