The origin of Free Primary Education (FPE) can be traced back to the 1948 Declaration of Human Rights where basic education was recognized as a human right. The current FPE programme was launched in 2003 and it led to an overwhelming enrolment of pupils at the primary level of education. Such a soaring enrolment is feared to have compromised the Kenya Certificate Primary Education (KCPE) performance, which is a key indicator of quality education. The study therefore aimed at determining the influence of high enrolment on; the ability of teachers to offer quality instruction; learning resources; management of pupils’ discipline and suggestion on how to improve FPE in light of KCPE performance. The paper assessed FPE on KCPE performance in Kaptama Division, Mt. Elgon District, Kenya. The researcher used descriptive survey design. A sample of 310 respondents consisting of 253 standard eight pupils, 40 teachers, 13 head teachers and 4 education officers was used. The main tools of data collection were a questionnaire and interview schedule. Document analysis was also used in the study. Data analysis involved the use of frequencies, percentages, tables, chart, graphs and description. The findings of the study established that implementation of FPE led to high enrolment which witnessed high pupil - teacher ratio and ill-discipline among pupils. It has also led to inadequate learning facilities (classrooms, desks and chairs), fewer tests for pupils which lack in content and depth and increased work load among teachers. This has in turn compromised KCPE performance. Constant inspection should be carried out by the Ministry of Education for the success of the programme.