The circumsporozoite protein (CSP), an essential protein that covers the surface of the Plasmodium sporozoite, is a key player in multiple stages of the parasite development within the mosquito and during interactions between sporozoites and mammalian hepatocytes. Here, we identify a novel function of Plasmodium berghei CSP: preventing parasite elimination during the early stages of hepatic infection, through its ubiquitylation at two lysine (K) residues, K252 and K258, located in the C-terminal domain. A Plasmodium berghei transgenic line lacking these lysine residues exhibited a significant decrease in hepatic infectivity, with parasites being eliminated 4 h after infection. The reduced infectivity correlated with an increased association of host autophagy markers, LC3 and LAMP1, to the parasitophorous vacuole membrane of the liver stage parasite. Notably, inhibiting the host autophagy pathway fully rescued the mutant parasites from elimination. Collectively, we reveal a strategy employed by Plasmodium to evade early clearance during hepatic infection, which relies on the ubiquitylation of specific CSP lysine residues, that results in reduced parasite elimination via host autophagic and lysosomal activity.