Fungal organisms are increasingly implicated in nosocomial urinary tract infections. Although Candida, Mucor and Aspergillus are the most commonly identified species, rare fungi are also occasionally observed to infect humans. Misidentification of the organism could result in treatment with an inappropriate antifungal agent, which could result in a florid fungal pyelonephritis. We report the occurrence of fungal pyelonephritis in a patient with stone disease secondary to Paecilomyces variotii. This case report emphasizes the need for an accurate identification of the organism and early and appropriate treatment.