In 2015, for the first time Tajikistan reported zero indigenous cases. The transmission of Plasmodium falciparum was interrupted in 2009.

By 1957, the campaign to eradicate malaria in Tajikistan had largely succeeded. Although sporadic cases occurred seasonally, the situation in the country remained relatively stable. In 1994, however, incidence quadrupled from the previous year. The deterioration of the situation in Tajikistan in the 1990s was linked to armed conflict, mass population movement across zones of intensive transmission (particularly Afghanistan, where malaria is endemic) and the disruption of public health services and vector control activities. The number of malaria cases reported in Tajikistan peaked in 1997, at nearly 30 000 cases.

Despite the fact that reported case numbers have dropped to zero since 1997, the risk of resumption of malaria in Tajikistan remains high, primarily in the districts bordering Afghanistan due to possible importation of cases and infected mosquitoes. This is coupled with the presence of local vectors and the existence of environmental and climatic conditions favourable to malaria transmission.

Malaria vectors in Tajikistan include Anopheles superpictus, An. pulcherimus, An. maculipennis, An. hyrcannus and An. martinius.