The safety of the learner is paramount to the provision of quality education in any country. While this is true for learners at all levels of education, it is particularly critical for learners at the basic education level in view of their relatively tender ages. Major concerns to schools is the increasing problem of drug abuse among learners. Although several studies worldwide have revealed that there is some relationship between Drug Abuse and pupil discipline, the same has not been established in areas like Homa Bay Sub County. It is against this backdrop that this study sought to establish the effect of drug abuse and substance on pupil discipline in primary schools in Homabay Sub County. Therefore the objective of the study was to establish the effects of drug and substance abuse on pupil discipline in primary schools. The study established that abuse of alcohol had a low effect on pupil discipline, Bhang had high effect, spirits had low effect, cigarettes had low effect, piritons had low effect and Postinor-2 pills had low effect. The Pupil discipline was in terms of failure to do homework, lateness, cheating in examinations, absenteeism, truancy, sexual harassment, pornography, bullying and insubordination which in most cases have culminated in arsons and stampedes in which pupils have lost their lives. The study recommends that all stakeholders in education should participate in eradicating drug and substance abuse among youth both at school and out of school.