Early detection of several skin-related neglected tropical diseases (skin NTDs)–including leprosy, Buruli ulcer, yaws, and scabies- may be achieved through school surveys, but such an approach has seldom been tested systematically on a large scale in endemic countries. Additionally, a better understanding of the spectrum of skin diseases and the at-risk populations to be encountered during such surveys is necessary to facilitate the process. We performed a school skin survey for selected NTDs and the spectrum of skin diseases, among primary schoolchildren aged 5 to 15 in Côte d’Ivoire, West Africa. This 2-phase survey took place in 49 schools from 16 villages in the Adzopé health district from November 2015 to January 2016. The first phase involved a rapid visual examination of the skin by local community healthcare workers (village nurses) to identify any skin abnormality. In a second phase, a specialized medical team including dermatologists performed a total skin examination of all screened students with any skin lesion and provided treatment where necessary. Of a total of 13,019 children, 3,504 screened positive for skin lesions and were listed for the next stage examination. The medical team examined 1,138 of these children. The overall prevalence of skin diseases was 25.6% (95% CI: 24.3–26.9%). The predominant diagnoses were fungal infections (n = 858, prevalence: 22.3%), followed by inflammatory skin diseases (n = 265, prevalence: 6.9%). Skin diseases were more common in boys and in children living along the main road with heavy traffic. One case of multi-bacillary type leprosy was detected early, along with 36 cases of scabies. Our survey was met with very good community acceptance. We carried out the first large-scale integrated, two-phase pediatric multi-skin NTD survey in rural Côte d’Ivoire, effectively reaching a large population. We found a high prevalence of skin diseases in children, but only limited number of skin NTDs. With the lessons learned, we plan to expand the project to a wider area to further explore its potential to better integrate skin NTD screening in the public health agenda. Integration of neglected tropical diseases (NTDs) into the public health agenda has been a priority in global health for the last decade. A common feature shared by several NTDs is skin involvement. Conditions within this group of NTDs have now been classified as skin NTDs to promote wider NTD integration. Several skin NTDs including leprosy, Buruli ulcer, yaws, and scabies are co-endemic in Côte d’Ivoire, West Africa. As children are vulnerable to these diseases, we carried out the first large-scale integrated, multi-skin NTD school survey in a rural district of this country. Our strategy of involving community healthcare workers and dermatologists effectively reached a large population. However, the detection of skin NTDs may have been limited because of the low schooling and attendance rate. We found a high prevalence of skin diseases among schoolchildren (26%), possibly due to poor socio-economic status and air pollution, which requires more attention. This high prevalence of skin diseases posed a challenge for our project as the need for medications and those with dermatological skills exceeded our capacity to reach our initial target population. Our study provides important lessons that will aid the framing of future school skin surveys in sub-Saharan Africa.