Penicillium is a ubiquitous fungus found in the soil, decaying plant material, freshwater, and other habitats. Although Penicillium species are generally harmless to humans, they can act as opportunistic pathogens in patients with a compromised immune system. Penicillium rolfsii is primarily known as an endophytic fungus with antioxidant and antibacterial properties, which has not been previously reported in culture tests from invasive human infections. This study reports the case of an eight-year-old boy who developed pneumonia following a near-drowning incident in a river, with P. rolfsii detected in sputum culture. The patient underwent cardiopulmonary resuscitation at the scene and was subsequently transferred to the intensive care unit at our hospital. Chest computed tomography confirmed severe aspiration pneumonia, and empirical treatment with ampicillin–sulbactam was initiated. Based on elevated β-D-glucan levels, voriconazole was added. Sputum cultures revealed the presence of Penicillium species, which were identified as P. rolfsii based on the β-tubulin gene sequence analysis. The treatment was successful, and the patient recovered. An environmental investigation of the plunge pool where the near-drowning incident occurred detected Penicillium species in the water samples. This is the first reported case of P. rolfsii being detected in culture tests of a human invasive infection, particularly in an otherwise healthy child. This case highlights the need for healthcare professionals to consider environmental fungi in Japanese river water as potential causes of invasive infections, such as pneumonia, particularly after near-drowning incidents.