Apicomplexan perforin-like proteins (PLPs) play key roles in the mechanisms associated with parasitic disease caused by genera such as Plasmodium (malaria) and Toxoplasma. They generally have been implicated in membrane pore formation or remodelling to help parasites invade in or exit from their respective environments. The mechanism(s) of pore-formation for these PLPs remain unknown. Here we focus on Plasmodium vivax PLP2, which is important during the symptomatic blood stage of the parasite life cycle. We show that recombinant full-length PvPLP2 is functional in pore formation. By imaging PvPLP2 on liposomes with negatively-charged lipids in vitro by cryo electron tomography, we found that PvPLP2 forms pores with various sizes. Most of these pores are formed in arc-sharped incomplete oligomeric assembly. By subtomogram averaging and classification, we solved the structure of PvPLP2 pores with various conformations at sub- nanometer resolution and modelled the MACPF domain and APCβ domain. These structures show clear density for the β-barrel formed by the MACPF domain and a convincing identification of the APCβ domain within the membrane environment. Our study reveals the first mechanism of pore formation for an apicomplexan PLP and provides insights into mechanism of membrane damage during parasite egress.