Collared pikas (Ochotona collaris) are cold adapted alpine lagomorphs of western Canada and Alaska, USA, that are vulnerable to direct and indirect effects of climate change. However, how and to what extent such changes influence persistence for this species is not well understood, particularly at fine spatial scales. Our goal was to evaluate how microclimate and microhabitat characteristics influence occupancy of collared pikas. We quantified thermal conditions during both summer and winter to test hypotheses about potential drivers of pika persistence. We recorded den occupancy and territory characteristics, including in situ measurements of den microclimate, across three study areas with contrasting climate gradients in southcentral and interior Alaska during 2017–2022. We examined changes in pika den occurrence by estimating annual colonization and extinction rates with a Bayesian dynamic occurrence model with forage availability, rock size, and multiple den temperature metrics as the explanatory variables. Our top model indicated that daily maximum temperature during both summer and winter best predicted den persistence and larger rocks had a moderating effect on warm summer den temperatures. This information helps to advance understanding about the mechanistic links between climate and population persistence for small mammal species under a rapidly changing arctic climate.