Glutathione peroxidase‐like thioredoxin peroxidase (Pf
TP
x
Gl
) is an antioxidant enzyme trafficked to the apicoplast, a secondary endosymbiotic organelle, in
Plasmodium falciparum
. Apicoplast trafficking signals usually consist of N‐terminal signal and transit peptides, but the trafficking signal of Pf
TP
x
Gl
appears to exhibit important differences. As transfection is a protracted process in
P. falciparum
, we expressed the N terminus of Pf
TP
x
Gl
as a
GFP
fusion protein in a related apicomplexan,
Toxoplasma gondii
, in order to dissect its trafficking signals. We show that Pf
TP
x
Gl
possesses an N‐terminal signal anchor that takes the protein to the endoplasmic reticulum in
Toxoplasma
—this is the first step in the apicoplast targeting pathway. We dissected the residues important for endomembrane system uptake, membrane anchorage, orientation, spacing, and cleavage. Protease protection assays and fluorescence complementation revealed that the C terminus of the protein lies in the
ER
lumen, a topology that is proposed to be retained in the apicoplast. Additionally, we examined one mutant, responsible for altered Pf
TP
x
Gl
targeting in
Toxoplasma
, in
Plasmodium
. This study has demonstrated that Pf
TP
x
Gl
belongs to an emergent class of proteins that possess signal anchors, unlike the canonical bipartite targeting signals employed for the trafficking of luminal apicoplast proteins. This work adds to the mounting evidence that the signals involved in the targeting of apicoplast membrane proteins may not be as straightforward as those of luminal proteins, and also highlights the usefulness of
T. gondii
as a heterologous system in certain aspects of this study, such as reducing screening time and facilitating the verification of membrane topology.