As peat-swamp forests in Borneo become progressively more fragmented, the species that inhabit them are increasingly threatened, notably the Endangered Bornean orang-utan Pongo pygmaeus. The area of a failed agricultural project known as the Mega Rice Project in Central Kalimantan, Indonesia, is composed of fragments of peat-swamp forest that are reported to contain orang-utans, although no comprehensive survey has previously been conducted. In a portion of this area we identified remaining forest fragments, using satellite imagery, and surveyed line transects for orang-utan sleeping nests to determine the density, abundance and distribution of the species. The total area of peat-swamp forest in the study area is 76,755 ha, 59,948 ha of which comprises patches at least as large as the home range of a female orang-utan (250 ha). We estimate a mean population density of 2.48 ± SE 0.32 individuals km−2 and a population of 1,700 ± SE 220 or 1,507 ± SE 195 individuals, based on a 25 and 250 ha minimum patch size threshold, respectively. This is c. 40–45% of the original population, and the fragmented population is unlikely to be viable in terms of long-term demographic and genetic stability. To ensure persistence of this population of orang-utans, direct conservation action to connect forest fragments and prevent further loss of peat-swamp forest will be required, including re-establishing the hydrological regime, reforesting barren areas and fighting fires.