Although common in plants, very few proteins are currently known to be localized to both the plastid and the mitochondrion in Plasmodium falciparum. One such protein is P. falciparum glutathione peroxidase‐like thioredoxin peroxidase (PfTPxGl) which we show, by immunofluorescence imaging and bioinformatics predictions, is localized to the apicoplast, the mitochondrion and the cytosol. The distribution of PfTPxGl was random in the population, with the protein localizing to any one organelle in some parasites and to both in others. It has been proposed that targeting to each organelle occurs via independent pathways that do not proceed via the Golgi. However, for PfTPxGl, both incubation at low temperature (15 °C) and Brefeldin A treatment reversibly blocked targeting to these organelles, suggesting the involvement of a novel trafficking route, most probably via the endoplasmic reticulum and Golgi. This idea is further supported by the lack of cleavage of the putative N‐terminal signal sequence of PfTPxGl, and this N‐terminal extension did not compromise PfTPxGl enzyme activity. In the context of evolution, a common pathway for the dual localization of a single gene product, such as the primitive endoplasmic reticulum–Golgi route, may have been retained as opposed to optimization for individual organellar import pathways. P. falciparum glutathione peroxidase‐like thioredoxin peroxidase (PfTPxGl), we show, is localized to the apicoplast, the mitochondrion and the cytosol by a non‐canonical pathway involving the ER and Golgi. The localization of PfTPxGl was heterogeneous in the population. In the context of evolution, the primitive ER‐Golgi route may have been retained as opposed to optimization for individual organellar import pathways