After treatment with antimicrobial chemotherapy for the elimination of urinary multidrug-resistant Pseudomonas aeruginosa (MDRP), a 48-year-old man with recurrence of bladder cancer complained of acute onset of dyspnea, and computed tomography revealed multiple nodular lesions in the lung. Candida albicans was isolated from both urinary and blood samples. He was diagnosed as having a septic pulmonary embolism caused by C. albicans. Fungal septic pulmonary embolism is a rare condition; however, we must be cautious about superinfection as a consequence of strong antimicrobial chemotherapy, and understand that the treatment for urinary MDRP is likely to be difficult.