The ontology-based information systems (IS) development is beneficial for analyzing, conceptual modeling, designing, and re-engineering complex IS to be semantically enriched and suitable for sophisticated reasoning on the IS content. On the other hand, fuzzy theory employment to handle uncertainty and fuzziness in IS becomes a hot topic in different practical domains, such as engineering, IS, computer sciences, etc. As such, ontology- and fuzzy-based IS are being developed. Consequently, there is a need to provide a comprehensive systematic mapping study (SMS) to build a structure on the ontology- and fuzzy-based IS field of interest and to grasp the main ideas. This paper presents findings of SMS, based on the papers extracted from Web of Science and Scopus and employing a bibliometric analysis tool to automate keyword mapping. We conclude this paper by summarizing the previous work and identifying possible research trends, which future investigations can extend. The main finding indicates that ontology and fuzzy logic contribute to ISs by expanding traditional IS to be intelligent IS, which is applicable for solving complex, fuzzy, and semantically rich (ontological) information collection, saving, processing, sharing, and reasoning in different application domains according to users’ needs in various countries.