The risk of opportunistic fungal infections is high in immunocompromised patients. The Penicillium genus is common and diverse in nature. However, it rarely causes infection in humans. Here, we reported a case of Penicillium janthinellum pneumonia in a systemic lupus erythematosus (SLE) patient, and the morphological characteristics of P. janthinellum were also described. The patient was a 64-year-old female. She had been diagnosed with SLE and membranous lupus nephritis 10 months previously. Her medications included methylprednisolone, cyclosporine, and hydroxychloroquine. She was admitted because of fever and diagnosed with pneumonia. P. janthinellum was isolated from sputum and bronchoalveolar lavage (BAL) samples. BAL fluid stained with multiple stains showed the presence of somewhat dichotomously branching septate fungal hyphae. P. janthinellum was identified, and its morphological features were described. Antibiotic susceptibility profiles showed that this strain had higher minimum inhibitory concentration (MIC) values in response to multiple antifungal drugs. The patient died 10 days after diagnosis. To the best of our knowledge, this report is the second to demonstrate that P. janthinellum causes infection and is the first to present an infection (pneumonia) caused by P. janthinellumi in an SLE patient. Clinical and laboratory personnel should be aware that the Penicillium genus also contains pathogenic bacteria that cannot simply be treated as contaminants, especially in immunosuppressed patients.