Improvement of learning outcomes in primary schools is one of the remaining challenges in the Kenyan education sector. Exam scores are commonly used globally to measure outcomes of learning activities of pupils in schools. This study underscores the importance of safe and protective learning environments to encourage pupil academic performance and examines whether or not experiencing sexual harassment in schools has a negative impact on pupil academic achievement. We employ CEM with the SACMEQ III dataset for 4,436 pupils in Kenya. Our result shows that pupils in schools where sexual harassment is reported, either from their peers or from their teachers, marked statistically significant lower exam scores than peers without experiences of sexual harassment, after controlling for covariates. As a conclusion, this paper suggests further analysis on the correlations between the experience of sexual harassment and pupil test scores with panel data from other SACMEQ participating countries. Stronger evidence generation on this theme would ultimately support better learning environments for pupils in primary schools in Sub-Saharan Africa.