Life Skills Education (LSE) is one of the subjects in Kenyan secondary school curriculum. One of the areas that secondary school students are taught is sexuality. However, adolescents continue to face significant sexuality related challenges; cases of early pregnancies, irresponsible sexual activities and STIs among boys and girls are common. Efforts have been made to address this problem but comprehensive and conclusive solutions have not been achieved. As such, this study examined the implementation of Life Skills Education programme on sexuality in selected secondary schools in Nairobi City County. The study adopted exploratory research design. Stratified random sampling was used to select 378 students and 26 teachers from 13 schools in Nairobi City County. The study utilized self-constructed questionnaires and interview schedules to collect data. Qualitative responses were coded to enable grouping into various thematic categories. Quantitative data was presented in form of percentages, means and standard deviations. Pearson’s product moment and Chi square analyses were used to establish any significant relationships. The study found that life skills education on sexuality is not effectively implemented in most schools. The study recommends that LSE teachers should put more effort to ensure effective implementation of Life Skills Education on sexuality.