In Rwanda, Neglected Tropical Disease (NTD) control program was established in 2007 and initial mapping was completed in 2008 before starting mass drug administration (MDA) against schistosomiasis (S. mansoni) and soil-transmitted helminths (STHs). This work presents data of S. mansoni in area which was initially omitted from MDA based on initial mapping. In 2011, children from Nkombo Island located in a district previously classified as low endemic for S. mansoni, were screened for S. mansoni (and STHs) using Kato-Katz method. Prevalence of S. mansoni (and STHs) was measured. In total 331 school children aged 10-19 years were involved. Prevalence of S. mansoni was found to be 62.1%, ranging from 28.6% to 77.9% across schools. Prevalence of S. mansoni in school children of Nkombo was found high. Regular MDA with praziquantel to all school-aged children and adults of the Island is warranted. For effective control, current school-based mapping strategy (WHO guidelines) is insufficient to identify all hot spots, should therefore be revised or supplemented with localized community-based surveys in areas where infection is likely to occur but available data do not indicate MDA.