INTRODUCTION: Skin neglected tropical diseases (NTDs), are endemic and under-diagnosed in many lower-income communities. The objective of this study was to determine the prevalence of skin NTDs and fungal infections in two primary schools and a community setting in rural Togo. METHOD: This was a cross-sectional study that took place between June-October 2021. The two primary schools are located on the outskirts of Lomé, the capital city. The community setting was Ndjéi, in north-east Togo. Study sites were purposively selected. Dermatologists examined the skin of study participants. Diagnosis of skin NTDs were made clinically. RESULTS: A total of 1401 individuals were examined, 954 (68.1%) from Ndjéi community, and 447 (31.9%) were children in the schools. Cutaneous skin infections were diagnosed in 438 (31.3%) participants, of whom 355 (81%) were in community settings. There were 105 observed skin NTDs (7.5%). Within the school setting, there were 20 individuals with NTDs (4.5% of 447 participants), and 85 NTDs (8.9%) from 954 community participants. Across all settings 68/1020 (6.7%) NTDs were in children, and 37/381 (9.7%) in adults. In addition, there were 333 observed mycoses (23.8% prevalence). The main cutaneous NTDs diagnosed were scabies (n = 86; 6.1%) and suspected yaws (n = 16, 1.1%). The prevalence of scabies in schools was 4.3%, and 7.0% in the rural community. One case of leprosy was diagnosed in each school and the rural community, and one suspected Buruli Ulcer case in the community. In the school setting, five (6%) children with a skin NTD reported being stigmatised, four of whom had refused to attend school because of their dermatosis. In Ndjéi, 44 (4.6%) individuals reported having experienced stigma and 41 (93.2%) of them missed at least one day of school or work. CONCLUSION: This study shows that the burden of scabies and skin infections such as superficial mycoses is high in the school and rural community settings in Togo, with associated presence of stigma. Improved health promotion and education across institutional and community settings may reduce stigma and encourage early reporting of skin infection cases to a health facility.