Fern species belonging to the oldest vascular plants have been widely used as traditional medicines by indigenous communities especially in the humid regions of South East Asia for thousands of years. Fungal endophytic associations with ferns have been identified through various mechanisms, resulting in host ferns' resistance to adverse conditions or growth enhancement. The highest potential of fungal endophytes to produce bioactive compounds and their biological properties has prompted research into endophytes associated with fern species. The purpose of this review is to provide an overview of the endophytic fungi isolated from fern plants with medicinal properties and highlight their potential as natural sources of novel bioactive compounds for agricultural and therapeutic applications. Further research is needed to investigate these fungal endophytes colonizing medicinal ferns in different ecological niches.