Tropical dry areas are often characterised by a lack of reptile abundance data. For example, in Burkina Faso, the population and ecological distribution of the gecko are poorly understood. Contributing to fill this gap, this study assessed the diversity, density and ecological distribution of geckos in the metropolitan area of Ouagadougou. The study was conducted between 2020 and 2022 using the direct count of individuals in 72 quadrats (each 25 × 25 m2) evenly distributed throughout the entire study area, from a random start. Two distinct species, Hemidactylus angulatus and Ptyodactylus sp. have been encountered. H. angulatus density was estimated as 0.000352 individuals/m2 (95% CI: ±0.000336) with a population estimate of 987,360 individuals (95% CI: ±942,480) in 2020; 0.000256 individuals/m2 (95% CI: ±0.000432) with a population estimate of 718,080 individuals (95% CI: ±1,211,760) in 2021; and 0.000368 individuals/m2 (95% CI: ±0.00048) with a population estimate of 1,032,240 individuals (95% CI: ±1,346,400) in 2022. Ptyodactylus sp. density was estimated as 0.010016 individuals/m2 (95% CI: ±0.004608) with a population estimate of 28,094,880 individuals (95% CI: ±12,925,440) in 2020; 0.012352 individuals/m2 (95% CI: ±0.005696) with a population estimate of 34,647,360 individuals (95% CI: ±15,977,280) in 2021; and 0.0144 individuals/m2 (95% CI: ±0.007136) with a population estimate of 40,392,000 individuals (95% CI: ±20,016,480) in 2022. The spatial distributions of both species were aggregative (dispersion index I = 3.81 for H. angulatus and I = 24.82 for Ptyodactylus sp.). Our study revealed that microhabitat is the resource axis typically partitioned by Ouagadougou geckos. The geckos of Ouagadougou follow the same pattern of available resource partitioning as African reptile communities.