Despite education being one of the basic human rights and an empowerment prerequisite, there are various factors that affect the provision of quality education in inclusive public primary schools in Kenya. This paper sought to examine the effects of teacher’s perception of school environment on academic performance of pupils with special needs in the inclusive classes. The paper adopted a descriptive survey design. The study used simple random to select to select the study respondents. Interview schedule and questionnaires were used for data collection. Cronbach alpha reliability coefficient of 0.716 and 0.784 was obtained for the teachers and pupils questionnaires respectively. Data collected was analyzed using descriptive statistics with aid of the Statistical Package for Social Sciences. Pearson’s correlation coefficient was used to establish the relationship between teacher’s perception of school environment and academic performance of pupils with special needs in inclusive classes. The findings showed that school environment had very significant effect on the academic performance of pupils with special needs in inclusive classes. The study concluded that teachers’ perception of school environment significantly influenced academic performance of learners with special needs in inclusive primary schools. The study recommended that school headteachers to enhance school environment that accommodate all learners for better academic performance.