The extensive use of anticoagulant rodenticides (ARs) to control rodent populations poses intoxication risks for wildlife: persistence of ARs in rodents can cause secondary exposure and poisoning of predators or scavengers. We investigated risk factors for wildlife exposure to ARs in the Parc National des Pyrénées (PNP), France, using a multivariable logistic regression analysis. A total of 157 liver samples were collected from carcasses of 10 mammal and three bird species found in the PNP between 2010 and 2018 and screened for presence of AR residues. First- and second-generation ARs were detected in more than 60% of red fox (Vulpes vulpes) and stone marten (Martes foina) samples and in around 40% of wild cat (Felis silvestris), European pine marten (Martes martes), American mink (Neovison vison), and Eurasian Buzzard (Buteo buteo) samples. Wildlife exposure to ARs was significantly associated with species having a regular consumption of small mammals (odds ratio [OR]: 2.5, 95% confidence interval [CI]: 1.1–5.8) being collected in the Ossau valley (OR: 2.5, 95% CI: 1.1–6.1) and between 2013 and 2015 (OR: 4.8, 95% CI: 2.0–11.7). We identified wild species that could be targeted for risk-based surveillance program for AR secondary exposure and determined high risk areas in which alternative measures should be applied for rodent control.