Rainbow trout, Oncorhynchus mykiss, were infected with Ichthyophonus sp. and held at 10°C, 15°C and 20°C for 28 days to monitor mortality and disease progression. Infected fish demonstrated more rapid onset of disease, higher parasite load, more severe host tissue reaction and reduced mean‐day‐to‐death at higher temperature. In a second experiment, Ichthyophonus‐infected fish were reared at 15°C for 16 weeks then subjected to forced swimming at 10°C, 15°C and 20°C. Stamina improved significantly with increased temperature in uninfected fish; however, this was not observed for infected fish. The difference in performance between infected and uninfected fish became significant at 15°C (P=0.02) and highly significant at 20°C (P=0.005). These results have implications for changes in the ecology of fish diseases in the face of global warming and demonstrate the effects of higher temperature on the progression and severity of ichthyophoniasis as well as on swimming stamina, a critical fitness trait of salmonids. This study helps explain field observations showing the recent emergence of clinical ichthyophoniasis in Yukon River Chinook salmon later in their spawning migration when water temperatures were high, as well as the apparent failure of a substantial percentage of infected fish to successfully reach their natal spawning areas.