Plasmodium falciparum, the causative agent of the deadliest form of human malaria, alternate between expressions of variable antigens, encoded by members of a multi-copy gene family named var. In var2csa, the var gene implicated in pregnancy-associated malaria, translational repression is regulated by a unique upstream open reading frame (uORF) found only in its 5’ UTR. We found that this translated uORF significantly alters both transcription and posttranslational protein trafficking. The parasite can alter a protein`s destination without any modifications to the protein itself, but instead by an element within the 5` UTR of the transcript. This uORF-dependent localization was confirmed by single molecule STORM imaging, followed by fusion of the uORF to a reporter gene which changes its cellular localization from cytoplasmic to ER-associated. These data point towards a novel regulatory role of uORF in protein trafficking, with important implications for the pathology of pregnancy-associated malaria.