In Japan, malaria is rare, and only a few institutions have the diagnostic capabilities to treat it. In falciparum malaria, the symptoms and signs of the disease are non-specific, and diagnostic delay in symptomatic patients can be fatal. Herein, we describe a case of falciparum malaria that achieved good outcomes in a patient who initially visited an institution in Japan that lacked malaria diagnostic resources. A female patient in her twenties was admitted to the emergency department with a high fever. She developed a fever three days after returning to Japan from Guinea, a malaria-endemic region. Additionally, she exhibited impaired consciousness, tachycardia, and tachypnea. Her laboratory results indicated an increased inflammatory response, thrombocytopenia, hyperbilirubinemia, and coagulopathy. Computed tomography revealed hepatic enlargement and splenomegaly. Based on these findings, malaria was suspected, and the patient was immediately referred to an infection-specialized hospital. There, the patient was diagnosed with falciparum malaria and was treated and discharged without increased severity. This case highlights the importance of promptly referring patients suspected of malaria who are returning from endemic areas to institutions with relevant diagnostic resources if required resources are unavailable.