Fuzzy Cognitive Maps (FCMs) have become an invaluable tool for healthcare providers because they can capture intricate associations among variables and generate precise predictions. FCMs have demonstrated their utility in diverse medical applications, from disease diagnosis to treatment planning and prognosis prediction. Their ability to model complex relationships between symptoms, biomarkers, risk factors, and treatments has enabled healthcare providers to make informed decisions, leading to better patient outcomes. This review article provides a thorough synopsis of using FCMs within the medical domain. A systematic examination of pertinent literature spanning the last two decades forms the basis of this overview, specifically delineating the diverse applications of FCMs in medical realms, including decision-making, diagnosis, prognosis, treatment optimisation, risk assessment, and pharmacovigilance. The limitations inherent in FCMs are also scrutinised, and avenues for potential future research and application are explored.