Student absenteeism and its effect on academic performance concerns all stakeholders in education. Schools in Nyandarua County have recorded high levels of absenteeism in their institutions. This study aimed at establishing the effect of absenteeism on academic performance of secondary school students in Nyandarua County Kenya. The target population of the study was 3,763 students from mixed public secondary schools. All hypotheses were tested at 95% significance level. The results indicated that student absenteeism affected academic performance and that the level of student absenteeism mattered in academic performance. It was found out that the main cause of student absenteeism was lack of school fees. The study also observed that many student counsellors did not treat student absenteeism as a problem requiring their intervention. The study further indicated that student age did not affect absenteeism and self-study habits of chronic absentees did not significantly affect their academic performance. Among the recommendations the study made included; provision of universal and free or affordable secondary education in Kenya.