Fungal microbes are important in the creation of new drugs, given their unique genetic and metabolic diversity. As one of the most commonly found fungi in nature, Fusarium spp. has been well regarded as a prolific source of secondary metabolites (SMs) with diverse chemical structures and a broad spectrum of biological properties. However, little information is available concerning their derived SMs with antimicrobial effects. By extensive literature search and data analysis, as many as 185 antimicrobial natural products as SMs had been discovered from Fusarium strains by the end of 2022. This review first provides a comprehensive analysis of these substances in terms of various antimicrobial effects, including antibacterial, antifungal, antiviral, and antiparasitic. Future prospects for the efficient discovery of new bioactive SMs from Fusarium strains are also proposed.