Introduction Harmful traditional practices violate and negatively affect the physical, psychological well-being and right of women and children. Nigeria has the third highest absolute number of women and girls who have undergone Female Genital Mutilation (FGM) worldwide. Aims To assess the harmful traditional practices on the under-five years children and associated factors in Sokoto, State, Nigeria. Methods A community based cross sectional study that was conducted in Sokoto State, Nigeria on 320 mothers of under-five year children from 1st January-31st March 2021. The study participants were selected using multi stage sampling method, after proportionate allocation of sample size, systematic random sampling method was used to get the study participants. A structured questionnaire was used to collect information on harmful traditional practices from the mothers of the eligible children. Data was analysed using SPSS version 22. Results The mean age of the children was 22.5 ± 17.7 months, there were 199(62.2%) males and 121(37.8%) females, and male to female ratio was 1.6:1. Eighty (25.0%) of the under five-year children were circumcised by traditional healers, 189(59.1%) had traditional uvulectomy, 86(28.9%) had female genital mutilation, while 11(3.4%) had scarification marks. The respondent’s educational status (p = 0.008) and (p = 0.001) were factors associated with the practice of FGM and circumcision respectively. Conclusion Harmful traditional practices are still prevalent in Sokoto. Government at all levels should embark on awareness creation programs on the dangers of these harmful traditional practices through mass media, schools, traditional leaders and religious places. Child protection laws should be implemented to curtail these harmful practices.