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Fire regimes are predicted to change under climate change, with associated impacts on species and ecosystems. However, the magnitude and direction of regime changes are uncertain, as will be species’ responses. For many species, how they respond will determine their medium-long-term viability. We propagate fire regime and species’ response uncertainties through a 50-year viability analysis of the great desert skink, Liopholis kintorei, in central Australia, characterizing fire regime change under three scenarios. Species’ response uncertainty was characterized with three competing models based on fire and habitat variables, fitted to 11 years of occupancy data. We evaluate fire management options for conserving the species, based on their robustness to uncertainty about fire and species’ response. Efforts to minimize the frequency and size of fires provides the most consistent improvements to species’ persistence. We show that disentangling important from unimportant uncertainties enables conservation managers to make more efficient, defensible decisions.