Private schools supplement the government’s efforts of providing education in Kenya. Pupils from private primary schools have been out-performing those from public primary schools at Kenya Certificate of Primary Education (KCPE). The purpose of this study was to establish and compare the trends of secondary school academic performance of students from private and public primary schools, in Forms 1, 2, 3 end year teacher made test, Mock and Kenya Certificate of Secondary Education (KCSE) examinations. The research design was causal-comparative with a study population comprising 2004 and 2005 form four students in Nakuru District. Stratified random sampling technique was used to select a sample of 240 students from 6 provincial schools out of the 19 provincial schools in Nakuru District. The six schools were randomly selected from the three categories of secondary schools; Boys only, Girls only and co-educational ( Mixed). The instruments used to collect data were the Students’ Questionnaire, Teachers’ Questionnaire, Students' Academic Performance summary form.The mean scores of students from private primary schools were below the mean scores of students from public primary schools.