We report an outbreak investigation of two fatal cases of autochthonous Plasmodium falciparum that occurred in Belgium in September 2020. Various hypotheses of potential source of infection were investigated. Based on the collected information, the most likely route of transmission was through an infectious exotic Anopheles mosquito that arrived via the international airport of Brussels or the Military airport Melsbroek and infected the cases who lived at five kilometres from the airports. Based on a genomic analysis of the parasites collected from the two cases, the most likely origin of the Plasmodium was Gabon or Cameroon. Further, the parasites collected from the two Belgian patients were identical-by-descent, which supports the assumption that the two infections originated from the bite of the same mosquito, during an interrupted feeding. Despite these cases, airport malaria remains a rare event. Yet, it has significant implications, particularly for the patient, as delayed or missed diagnosis of the cause of illness often results in high rates of complications and mortality. Therefore, to prevent such severe or fatal outcomes, a number of public health actions are suggested including increased awareness among health practitioners especially those working in the vicinity of airports and increased surveillance of exotic mosquito species at airports.