The southern cassowary Casuarius casuarius johnsonii L. is an endangered flightless bird from northern Australia. The cassowaries’ rainforest habitat has been extensively cleared, and the population primarily exists within discrete protected areas. They do, however, venture outside the reserves into modified landscapes, and it is here they are exposed to threatening processes. We used GPS-based telemetry and the adaptive local convex hull (a-LoCoH) non-parametric kernel method to define the relationship between cassowary home range (HR) and a protection-area network. The study showed that: (1) females had a larger HR than males; (2) overlapping HR occurred between but not within the sexes; (3) HRs of the same sex partitioned along defined boundaries; and (4) the current protected areas only encompassed core HR for the inhabiting cassowaries. This information was incorporated within a spatial-conservation-prioritisation analysis to define the relative cost:benefit relationship for protecting the currently non-protected land utilised by the cassowaries. The results showed that the current reserve system may accommodate up to 24 adult cassowaries, only offering HR protection at the 40 to 60% a-LoCoH. This could be raised, relatively cheaply (1.2-fold the current costs), to 70% a-LoCoH for all birds by protecting adjacent forested areas on private land. Protection beyond the 70% a-LoCoH, however, required protection of large expanses of agricultural land, resulting in an exponential increase in monetary cost (5.1-fold). We argue that total HR protection for the cassowaries was an unfeasible conservation option, but protection of core habitat was achieved relatively cheaply. Combining core HS protection with target incentives to landowners of adjacent cleared land may be the most cost-effective conservation strategy for C.c. johnsonii.