Understanding factors that determine haemosporidian prevalence is critical in predicting how parasite and avian host populations will respond to environmental change. Here, we used molecular screening of blood samples from migrating northern saw‐whet owls Aegolius acadicus in eastern North America to characterize haemosporidian infections and examine parasite prevalence with respect to abundance of migrants, timing of migration, climatic conditions at the breeding grounds, and avian host age. We identified three haemosporidian genera (Leucocytozoon, Plasmodium, and Haemoproteus) and discovered a new lineage of Leucocytozoon that is thus far specific to the northern saw‐whet owl. We found no significant relationship between parasite prevalence and northern saw‐whet owl abundance or timing of migration. After‐hatch‐year birds were significantly more likely to be parasitized by Leucocytozoon than hatch‐year birds, whereas prevalence of Plasmodium was higher in hatch‐year birds. Of the three climatic variables analyzed at owl breeding grounds (temperature, precipitation, and snowpack days), lower average annual temperatures significantly increased the chance of a bird being parasitized by Leucocytozoon; no significant temperature‐dependent relationship was found for Plasmodium. This study contributes to our general understanding of the relationship between parasite prevalence and host density, host age, resource abundance, and abiotic factors such as temperature and precipitation.