Skeletal muscle is known to be damaged by falciparum malaria via sequestration of infected erythrocytes. We present a case of rhabdomyolysis caused by Plasmodium knowlesi infection. The patient had fever, myalgia, and muscle weakness 5 days after returning to Japan from Palawan, the Philippines. Blood test revealed thrombocytopenia and an elevated creatine kinase level. Although rhabdomyolysis resolved with fluid therapy, fever of 24-hour cycle continued and thrombocytopenia intensified. On day 7 of illness, Giemsa-stained thin blood smear revealed malaria parasites, with a parasite count of 2,380/μL, which were morphologically indistinguishable between P. knowlesi and Plasmodium malariae. Rapid diagnostic test showed a negative result. The pathogen was later confirmed to be P. knowlesi by nested polymerase chain reaction (PCR). The patient was successfully treated with artemether/lumefantrine. This case suggests that knowlesi malaria might be able to cause skeletal muscle damage.