With an estimated < 50 adult individuals remaining, the Critically Endangered Balkan lynx Lynx lynx balcanicus is one of the rarest, most threatened and least-studied large carnivores. To identify priority conservation areas and actions for the subspecies, during 2006–2014 we conducted 1,374 questionnaire surveys throughout the potential range of the Balkan lynx to (1) evaluate human–lynx interactions and identify potential threats, and (2) determine the probability of site use in 207 grid cells through occupancy modelling. Human–lynx interactions were related mainly to poaching of lynx, and damage to livestock by lynx. Poaching was intense throughout the potential range of the subspecies, apparently having affected 50–100% of the total estimated extant population. Damage to livestock was recorded only in relation to sheep, mainly in the southern part of the lynx's potential range. Occupancy modelling indicated 108 grid cells with high probability of site use, which was affected mainly by increased terrain ruggedness and reduced forest cover. Based on the combined results of our study we identified five priority areas for conservation, as well as in situ habitat protection, community participation in the conservation of the subspecies, and the improvement and implementation of the existing legal framework as the priority conservation actions for the Balkan lynx.