Schistosoma malayensis is a schistome parasite. It was first described in 1988 in Peninsular Malaysia and appears to be a zooenotic infection. The species is named after the country of Malaysia. The natural vertebrate host is van Müller's rat (Rattus muelleri).

Among humans exposed to this parasite the lifetime incidence appears to be 5-10%.. The disease has been little studied and it is currently considered to be a relatively minor public health problem.