Millardia kondana is a Critically Endangered species of rat, known only from four localities in India. All these sites were facing growing threats from grazing, fire, and infrastructure-, housing-, and tourism-development. Therefore, we conducted this study to examine the spatiotemporal variation in population density and size and habitat preference of M. kondana. We carried out live trapping of M. kondana at three sites and recorded microhabitat covariates which were likely to influence its abundance. Spatially explicit capture-recapture models (SECR) were used to estimate density of the species. In total, 210 individuals of M. kondana were captured for 301 times in 2700 trap night efforts with trapping success of 11.15 rats/100 trap nights. Density estimates (2.01–10.76 rats/ha) and population estimates (20.24–246.34 individuals) showed substantial spatiotemporal variation. M. kondana appeared to be fast breeding species with a short life span. Model predictions indicated that the species preferred open habitats. Its abundance was positively influenced by increasing perennial herb density (PHD) and herb height (HH). Thus, the conversion of open habitats into forested habitats or human settlements need to be stopped to conserve this species.