Background Tungiasis is a relatively frequent ectoparasitosis in low-income settings, yet its morbidity and social impact are still not well understood due to the scarcity of information. In Rwanda, data on the magnitude and conditions leading to the tungiasis is rare. This study sought to determine the prevalence and factors associated with tungiasis among primary school children in Rwandan setting. Method A descriptive cross-sectional study utilising systematic random sampling method was adopted to select 384 children from three primary schools. From July to October 2018, data were collected on socio-demographic characteristics of children, parents, and households. Logistic regression was applied to analyse socio-demographic factors associated with tungiasis with a level of significance set at P -value< 0.05. Results Prevalence of tungiasis among three primary schools was 23%. Factors associated with tungiasis included walking barefoot (AOR: 78.41; 95% CI: 17.91–343.10), irregular wearing of shoes (AOR: 24.73; 95% CI: 6.27–97.41), having dirty feet (AOR: 12.69; 95% CI: 4.93–32.64), wearing dirty clothes (AOR: 12.69; 95% CI: 4.18–38.50), and living in a house with earthen plastered floor (AOR: 28.79; 95% CI: 7.11–116.57). Children infected with tungiasis attended class less frequently (AOR: 19.16, 95%CI: 7.20–50.97) and scored lower (AOR: 110.85, 95%CI: 43.08–285.20) than those non-infected. The low school attendance and poor performance could be partly explained by difficulty of walking, lack of concentration during school activities, and isolation or discrimination from classmates. Conclusion Tungiasis was a public health challenge among school going children in a rural Rwandan setting. This study revealed that children affected with tungiasis had poor hygiene, inadequate housing environments and consequently poor school attendance and performance. Improving socio-economic conditions of households with special emphasis on hygiene of family members and housing conditions, would contribute to preventing tungiasis. Electronic supplementary material The online version of this article (10.1186/s12889-019-7481-y) contains supplementary material, which is available to authorized users.