Estimating the population size of threatened species is problematic and has biases because of a lack of validation data. The Javan Hawk-Eagle (Nisaetus bartelsi) is an endangered raptor endemic to the remnants of natural rainforests of Java, Indonesia. We aimed to improve the accuracy of population estimates through a combination of current habitat distribution modeling and patch occupancy surveys. Higher-resolution data sources (improved from 250 m to 30 m) were used in a predicted probability model using logistic regression. Patch occupancy surveys were conducted in habitat patches identified from a predictive analysis and field validation results after 2008. We estimated population sizes only in occupied patches ≥20 km2 (size based on Javan Hawk-Eagle home-range size). The area of suitable habitats currently totaled 10,804 km2, as calculated from the results of the 2019 predicted probability model (9106 km2) and field validation (1698 km2). The predicted area in 2019 decreased by 6.5% (638 km2) from that in 2008. We detected small suitable patches because of improvements in data resolution. The patch occupancy survey validated 44 of the 74 patches (59.5%) in the current habitat distribution. We confirmed that 38 patches (10,166 km2) were occupied by Javan Hawk-Eagles, and we estimated the population to be 511 ± 3.1 (SE) pairs. This apparent population increase is attributable to improved methodologies in predicting habitat distribution and estimating population size.