This species is seriously threatened by logging (both legal and illegal), wholesale conversion of forest to agricultural land and oil palm plantations, and fragmentation by roads. Animals are also illegally hunted and captured for the international pet trade but this appears to be more a symptom of habitat conversion, as orangutans are killed as pests when they raid fruit crops at the forest edge.

A new threat is the Ladia Galaska road network in Aceh province, which if legitimized by the government will rapidly fragment most of the populations listed above. Another major concern is the re-issuing of logging permits for large tracts of forest in Aceh.

An assessment of forest loss in the 1990s concluded that forests supporting at least 1,000 orangutans were lost each year within the Leuser Ecosystem alone (van Schaik et al. 2001). These loss rates subsequently dropped dramatically during major civil conflict in the province, and the imposition of a moratorium on logging in Aceh. A peace deal negotiated in 2005 led to political stability and many new applications to open up logging concessions and palm oil estates in orangutan habitat.

In parts of North Sumatra orangutans are also still hunted on occasions for food.