Life processes of ectothermic vertebrates are intimately linked to the temperature of their environment, influencing their metabolism, reproduction, behaviour, and immune responses. In amphibians infected by the generalist chytrid pathogen Batrachochytrium dendrobatidis (Bd), host survival, infection prevalence, and infection intensity are often temperature- and/or seasonally-dependent. However, the transcriptional underpinnings of thermal differences in infection responses are still unknown. Measuring the impact of temperature on host responses to infection is a key component for understanding climatic influences on chytrid disease dynamics. Bd-responsive gene pathways in frogs are well documented, but our understanding of salamander immune expression profiles during infection with chytrids remains limited. We characterize the transcriptomic responses of Plethodon cinereus using RNAseq by comparing skin and splenic gene expression of individuals uninfected, succumbing to Bd infection, and naturally cleared of Bd infection at three temperatures. We propose amphibian temperature-dependant susceptibility to Bd is likely driven by shifts in expression of innate and adaptive immune axes. Our study shows increased expression of transcripts associated with inflammation at cooler temperatures and a shift towards increased expression of adaptive immune genes, including MHC, at higher temperatures. In the face of climate change, and as concerns for the spread of emergent chytrid pathogens increase, our results provide important functional genomic resources to help understand how these pathogenic fungi may continue to affect amphibian communities globally in the future.