Whitebark pine populations are declining nearly range-wide, primarily from the exotic fungal pathogen that causes white pine blister rust (WPBR). Climate change is expected to exacerbate these declines by decreasing climatically suitable areas. Planting WPBR-resistant seedlings is a key restoration action, but it is costly, time consuming, and labor intensive. Direct seeding—sowing seeds rather than planting seedlings—may reduce costs and open remote areas to restoration; however, its efficacy remains largely unexplored. In this case study, we estimated the annual survival rates (ASR) of seedlings grown from directly sown seeds, and the effect of elevation zone and microsite type on survival. For five years we monitored 184 caches containing one or more seedlings within one study area in the Greater Yellowstone Ecosystem. Seed caches were originally stratified between subalpine forest and treeline and among three microsite types defined by a nurse object: Rocks, trees, and no object. To estimate ASR, we selected the most parsimonious model of a set using AICc. ASR was best described by elevation zone and year and ranged from 0.571 to 0.992. The odds of seedling survival were 2.62 times higher at treeline than in subalpine forest and were 4.6 to 36.2 times higher in 2016–2018 than 2014. We estimated the probability that a whitebark pine seed cache would contain one or more living seedlings six years after sowing to be 0.175 and 0.0584 for treeline and subalpine caches, respectively. We estimated that 1410 and 4229 caches ha−1 would need to be sown at treeline and in subalpine forest, respectively, to attain target restoration densities of 247 established trees ha−1. Our findings, although based on one study area, suggest that climate change may be increasing treeline regeneration, and that direct seeding may be a viable restoration option and climate change mitigation tool for whitebark pine.