Management of sewage sludge is of ongoing concern because this waste product is generated continuously and contains high levels of harmful constituents. Among these constituents, fungal pathogens are of increasing concern. Vermicomposting can reduce the amounts of bacterial pathogens in sewage sludge; however, information about the effects of earthworms on fungal pathogens is limited or non-existent. We therefore aimed to determine whether vermicomposting can control fungal pathogens present in sewage sludge. Using next-generation sequencing techniques, we characterized fungal communities in sewage sludge from eight wastewater treatment plants (WWTPs) and in casts (feces) of earthworms feeding on sewage sludge. Fungal communities in earthworm casts primarily included taxa that were absent from sewage sludges, indicating a significant change in fungal composition. Changes in fungal diversity depended on the source of sewage sludge (WWTP). All of the sewage sludges contained low levels of fungal pathogens, most of which were significantly reduced or eliminated by earthworms, such as , , and . Moreover, earthworm gut transit enhanced beneficial (saprotrophic) fungi like , , and . Overall, digestion of sewage sludge by earthworms alone generated a mainly pathogen-free fungal community with a high proportion of saprotrophic taxa, which would enhance nutrient cycling rates.