Medical question answering (QA) systems have become a popular research topic in medical information services due to their importance for professionals, physicians and patients. The aim of this article is to explore medical question answering papers focusing on the datasets, methods and application in deep learning framework. We searched three databases: PubMed, IEEE explore and Google scholar, and forward and backward citations from 2022 up to 2025. Our first search results 88 studies, 40 of which are included for in-depth analysis following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) methodology. We anticipate several challenges including language, contextual and cultural difference for QA tasks.