In vitro trials investigating the effects of albendazole and triclabendazole anthelmintics on the growth profiles of the egg-parasitic fungi Paecilomyces lilacinus and Verticillium chlamydosporium were undertaken. In addition, in vivo trials were conducted in goats fed on millet grain cultures of each fungus and administered albendazole and triclabendazole anthelmintics. In vitro growth revealed V. chlamydosporium to be more sensitive to albendazole compared to P. lilacinus. In contrast, triclabendazole had the least inhibitory effect on in vitro growth of both P. lilacinus and V. chlamydosporium. Similar to albendazole, growth of P. lilacinus was more vigorous at 0.5 ppm concentration of triclabendazole. Efforts to re-isolate these egg-parasitic fungi from faeces of goats fed on fungal millet grain cultures before and following single intraruminal administration of albendazole and triclabendazole showed that P. lilacinus was not able to be re-isolated from the faeces at any sampling period. In contrast, V. chlamydosporium was able to be re-isolated from the faeces at all of the sampling periods except for the samples taken at 8–18 h and 18–24 h after administration of albendazole and triclabendazole, respectively. Lack of fungal activity at these times coincided with peak plasma availability of anthelmintics and suggests faecal levels of drugs were also high at these times and impacted negatively on fungal viability.