Most studies on community perceptions toward malaria have been undertaken in high-endemic countries, and studies from low-endemic countries have only recently been published. Similar information is also needed for hypoendemic countries such as Indonesia, to cope with the persistence of foci-endemic malaria in these regions. An applied qualitative method, Rapid Assessment Procedures, was employed during a 3-month intensive data collection period in Jepara district, Central Java province. Data were retrieved from 38 free-listings, 28 in-depth interviews, seven focus group discussions and unstructured observation. Qualitative thematic content analysis was applied. In this community, malaria (known as katisen or panas tis) was considered a common but minor illness. Insufficient understanding of malaria signs and symptoms in the subvillages likely leads to delay in illness recognition and treatment; not surprisingly self-treatment is common and the dosage most likely below the recommended dose. The health center was used but when it did not work, most people would shift back to traditional services due to cost considerations. Low understanding and acceptance of the causal link between the mosquito and malaria, likely leading to poor comprehension of preventive activities, as well as confusion of malaria with dengue fever, were identified. In conclusion, this study highlights a consistent gap between the common understanding and the biomedical description of malaria. If case management continues to be the main strategy in malaria control program, the emic perspective of the people must be well-integrated into the program. Likewise, interventions to improve home-treatment should also be developed.