Forty years of deforestation and logging have degraded and fragmented much of Borneo’s lowland forest. This poses a threat to the island’s unique biodiversity, which can be exacerbated by hunting and killing. Although orangutans sometimes persist in small forest patches, it is unclear if such highly fragmented habitats can sustain viable populations, and whether they facilitate movements across modified landscapes over the long-term. Since longitudinal population data are unavailable, inferences must be made from modelling. We applied a spatially-explicit individual-based model to predict the potential long-term viability of orangutan populations across Borneo. Specifically, we examined how population dynamics and dispersal could be affected by the loss of habitat fragments and removal of individuals through hunting, retaliatory killings and capture and translocation. Small forest fragments facilitated orangutan movement, increasing the number of individuals settling in non-natal patches. However, large rivers remained a substantial barrier, and limited the capacity of orangutan populations to recover from decline. Orangutan populations were also highly vulnerable to even small amounts of offtake, with annual removal of >2% diminishing the positive role that small fragments played in sustaining population connectivity and long-term viability. Our results imply that orangutan populations could grow and recover from recent declines across Borneo if further habitat loss within human-modified landscapes is minimized. However, this will only be achievable if efforts are made to reduce the removal of orangutans by promoting coexistence with people, limiting killings, and only engaging in translocations in rare cases where no suitable alternative exists.