Leptospirosis is a zoonotic disease caused by Leptospira, which is transmitted through infected mammalian species, including small mammals. However, the prevalence of pathogenic Leptospira spp. in small mammals, particularly between different site categories in the eastern part of Peninsular Malaysia, is still underexplored. Therefore, in this study, we aim to determine the species composition of small mammals and the prevalence of pathogenic Leptospira spp. between different site categories from Dungun, Terengganu. We selected five case sites (leptospirosis cases were recorded) and five control sites (no leptospirosis cases were recorded) in Dungun, Terengganu, based on previous reports by the Ministry of Health (MOH) Malaysia (2016-2020). For three consecutive nights, 100 cage traps were used for each trapping session between September 2021 and January 2022. In addition, DNA from kidney samples of captured individuals was extractedfor the Polymerase Chain Reaction (PCR) detection of pathogenic Leptospira spp. Overall, 89 individuals from five species were captured (6.43% trapping success), consisting of Rattus norvegicus (n = 39), Rattus rattus (n = 27), Suncus murinus (n = 11), Rattus exulans (n = 10) and Tupaia glis (n = 2). Out of 89 individuals captured, 14 tested positive with a 15.7% (n = 14/89) prevalence rate. R. norvegicuswas the most dominant captured species and had the highest number of infected individuals with pathogenicLeptospira (20.5%, n = 8/39). The statistical analysis revealed a significant difference in pathogenic Leptospira spp. between case and control sites (P < 0.05), with control sites recording higher positive individuals (78.6%, n = 11/14) compared to case sites (21.4%, n = 3/14). However, no significant differences were observed between species and sex (P > 0.05). The results of the study show that the monitoring of leptospirosis cases should not only focus on case sites but also on the control sites, even if there were no reports of leptospirosis cases in the area, in order to prevent outbreaks of this disease in the future.