Summary Many pathogens infect a wide range of host species. However, variation in the outcome of infection often exists amongst hosts and is shaped by intrinsic host traits. For example, contact with pathogens may trigger changes in hosts directed toward preventing, fighting, or tolerating infection. Host responses to infection are dynamic; they change over time and vary depending on health, condition and within the context of the environment. Immunological defences are an important class of responses that mediate host–pathogen dynamics. Here, we examined temporal patterns of immunity in two amphibian species, Pacific tree frogs (Pseudacris regilla) and Cascades frogs (Rana cascadae), exposed to control conditions or experimental inoculation with the emerging infectious fungal pathogen, Batrachochytrium dendrobatidis (Bd). For each species, we compared bacterial killing ability of blood and differential white blood cell counts at four different time‐points after pathogen inoculation. We also quantified infection load over time and monitored survival. We detected qualitative and quantitative differences in species responses to Bd. Pseudacris regilla exhibited an increase in infection load over time and 16% of Bd‐exposed animals died during the experiment. Tree frogs lacked robust treatment differences in immune responses, but Bd‐exposed P. regilla tended to display weaker bacterial killing responses than unexposed control animals. Neutrophil counts did not vary consistently with treatment and lymphocytes tended to be less abundant in Bd‐exposed animals at the later sampling time‐points. In contrast, Bd‐exposed R. cascadae exhibited a decrease in infection load over time and no mortality occurred in the Bd treatment. Bd‐exposed Cascades frogs showed stronger bacterial killing responses and an elevated number of neutrophils in blood when compared with control animals, and both responses were upregulated within 48 h of pathogen exposure. Lymphocyte counts did not vary significantly with treatment. Although only statistically significant in Cascades frogs, neutrophil:lymphocyte ratios showed a trend of being elevated in Bd‐exposed animals of both species and are indicative of pathogen‐induced physiological stress. Our results suggest that variation in systemic immunological responses of two syntopic amphibian species is associated with and may contribute to differential patterns of survival and infection load during exposure to the chytrid fungus. Species variation in immunological responses as soon as 48 h after pathogen exposure suggests that initial host–pathogen interactions may set the stage for subsequent infection and disease progression. Variation in host responses can drive disease dynamics and comparative studies of host responses to pathogens are critical for making predictions about pathogen emergence, spread and persistence.