Northwest African cheetah populations have declined precipitously, with expert opinion estimating that <420 individuals persist across parts of Algeria, Benin, Burkina Faso, Chad, Niger and Mali. However, no reliable density estimates exist in the remaining subspecies strongholds throughout the Sudano‐Sahel Zone, including the W‐Arly‐Pendjari Complex and Greater Zakouma Ecosystem within the Bahr/Salamat landscape. Camera trap surveys were combined with spatially explicit capture–recapture methodologies in both regions to estimate the cheetah density and detectable demographic composition of these populations. Following 15 429 camera trap nights, we detected nine individuals during the dry season and four individuals during the wet season in Pendjari (2021), nine individuals (dry season; 2023) in Zakouma and none in Siniaka Minia. Cheetah densities were thus estimated at 0.17–0.24 and 0.37 cheetah per 100 km2 in Pendjari and Zakouma, respectively. While marginally higher than predicted, such low‐density estimates are concerning in the last remaining habitats harbouring this critically endangered subspecies. Considering the substantial contraction of regional cheetah distribution, we estimate an overall population size of 68 ± 29 individuals across the studied areas. These novel estimates are among the lowest formally determined densities throughout cheetah range in Africa, where a high frequency of people and livestock detected on camera traps highlight the ongoing risks to large carnivores in these protected areas. Subsequent management recommendations include implementation of the established regional conservation strategies that encompass the distributional range of these cheetah, continuous monitoring of populations, genetic analyses to inform management, curbing illegal trade and increasing international awareness around the plight of the subspecies.