Malaria control project was first initiated in Nepal in 1954 with the support from USAID (then USOM). The objective of the project was to study malaria mainly in Terai belt of central Nepal. In 1958, national malaria eradication program, was launched with the objective of eradicating malaria from the country within a stipulated time period. Due to various reasons the eradication concept was reverted to control program in 1978. Following the call of WHO to revamp the malaria control programs in 1998, Roll Back Malaria (RBM) initiative was launched to address the perennial problem of malaria in hard-core forestes, foot hills, inner Terai and valley areas of the hills, where more than 70 percent of the total malaria cases of the country prevail. The high risk of acquiring the disease is attributed to the abundance of vector mosquitoes, mobile and vulnerable population, relative inaccessibility of the area, suitable temperature, environmental and socio-economic factors. Currently malaria control activities are carried out in 65 districts at risk of malaria. The recent micro-stratification of the malaria risk areas and population up to most peripheral level administrative units, i.e. VDCs, are divided into four different categories based on number of malaria cases, geo-ecology promoting vector breeding and vulnerability due to migration and population movements.
Based on the micro-stratification performed in 2012, approximately 13.02 million population (47.9%) live in malaria endemic VDCS. Out of the estimated total population living in endemic areas, 0.98 million (3.62%) live in high risk VDCs, 2.66 million (9.8%) live in moderate risk VDCs, and 9.38 million(34.52%) live in low risk VDCs. High and moderate risk VDCs show an API more than 0.5/1000 population, low VDCs less or equal to 0.5/1000 API but different from zero. A total population of 14.13(52.1%) is estimated to live in VDCs where malaria transmission is absent. The high risk areas consist of foothills and river belts, forest fringe areas, forests of Terai area, inner valleys and some Terai districts. Low risk VDCs lie in plain cultivated outer Terai, mountain , and mountain river valleys.