High anthropogenic pressure not only affects individual species, but also has a negative impact on overall ecosystem health and its resilience capability, especially in the ecosystem transition zone, such as “timberline ecotone”. Timberline ecotone in western Himalaya is currently facing dual threat due to climate change and anthropogenic pressures. The present study aims to enhance our understanding about how various mammal and bird species use this ecotone across seasons and gradient of anthropogenic pressure, using standard animal abundance estimation method in the state of Uttarakhand, India. Ten mammalian species, five birds of prey, four pheasant, and fifty-three small bird species were found to use timberline ecotone during different seasons. The timberline ecotone experiences high anthropogenic pressure during summer and monsoon. The abundance of mammal such as Himalayan musk deer (β = − 1.62 ± 0.50, P < 0.01) and pheasant such as Himalayan monal (β = − 0.38 ± 0.15, P < 0.01) were found to be negatively influenced by wood cutting, livestock grazing. The density and species richness of small birds were comparatively higher in moderately disturbed sites than that of highest or least disturbed sites. In addition, the small bird species composition varied significantly across sites with different anthropogenic pressure. This study revealed the differential impact of anthropogenic pressure on various mammalian and bird species, which utilized timberline ecotone seasonally or year round. Furthermore, the result of the present study also indicated faunal species (e.g., Himalayan musk deer), which could be used as indicator species to understand impact and magnitude of anthropogenic pressure on timberline ecotone.