Most hemoparasites hosted by wild birds appear to be harmless, but most of the blood parasite studies in avian wildlife are mainly focused on passerines or migratory species. This study aimed to assess the occurrence of blood parasites in nocturnal raptors (Strigiformes order) and their effect on hematological parameters. A total of 134 blood samples were collected during a four-year period for hematological analysis and hemoparasite detection and quantification by microscopical examination of the samples. Overall, the occurrence of hemoparasites was 35.1%, with Leucocytozoon being the most frequently detected (32.1%), followed by Haemoproteus (11.2%), Trypanosoma and Plasmodium (2.2% each). Among the different bird species, the Eurasian eagle-owl (Bubo bubo) showed the highest blood parasite positivity (94.7%). In barn owls, the positive birds displayed a lower hematocrit measurement and body condition score than the non-parasitized ones (p = 0.007 and p = 0.005, respectively), especially those parasitized by Leucocytozoon. Moreover, the analysis of the magnitude of this association revealed that the presence of hemoparasites is five times more frequent in barn owls with a 2/5 body condition score. Despite the host–parasite coevolution in Strigiformes, our results show a correlation between the presence of hemoparasites and some health parameters, including blood parameters.