Pathogenic fungi are fungi that cause disease in humans or other organisms. Although fungi are eukaryotic, many pathogenic fungi are microorganisms. Approximately 300 fungi are pathogenic to humans; their study is called "medical mycology ". Fungal infections are estimated to kill more people than either tuberculosis or malaria—about two million people per year.

In 2022 the World Health Organization (WHO) published a list of fungal pathogens which should be a priority for public health action.

Markedly more fungi are pathogenic to plant life than those of the animal kingdom. The study of fungi and other organisms pathogenic to plants is called plant pathology.