Plasmodium falciparum, the causal agent of malaria, is frequently exposed to changes of temperature during its life cycle such as the cyclical fever episodes that occur in many infected patients. Different parasite lines vary in their survival rates to high febrile temperatures, but the mechanism by which some are more resistant than others remains unknown. Next generation sequencing analysis of control and heat shock-adapted parasites revealed a point mutation in pf13_0235 (designated as ap2-hs) only present in the fever sensitive parasites, a result that was later validated in a collection of ten parasite subclones. This gene encodes an ApiAP2 transcription factor predicted to regulate the expression of heat shock protein (hsp) genes, which place AP2-HS as a candidate regulator of heat shock response. We used heat shock assays to simulate fever episodes in vitro comparing sensitive versus resistant parasites, and subsequently analysed hsp mRNA levels. Resistant parasites showed an immediate increase of hsp genes expression, whereas this response was delayed and much lower in sensitive parasites. Thus, AP2-HS plays an important role as the master regulator of heat stress response, which is the first protective transcriptional response described in P. falciparum blood stages.