The purpose of this study was to investigate the relationship between student cognitive engagement and academic achievement of secondary school students of Manga Sub County, Nyamira County, Kenya. The study was hinged on the Self Determination theoretical perspective. The mixed methods approach was employed, and within it, the concurrent triangulation design was adopted. From the target population of 1750 form four students, 35 Principals and 35 Guidance and Counselling teachers, 312 students (out of 316 expected), 11 Principals and 11 Guidance and counselling teachers were randomly sampled for the study. Questionnaires were used to collect data from the students, while interview schedules were used to collect data from Principals and Guidance and Counselling teachers. The validity of the research instruments was determined by experts from the department of Psychology and Educational Foundations of Jaramogi Oginga Odinga University of Science and Technology. Reliability was ascertained by the internal consistency method using Cronbach’s alpha, and a reliability coefficient of r above 0.7 was obtained for the questionnaire. Inferential statistics from quantitative data were analyzed using Pearson’s Product correlation and regression analysis with the aid of the statistical package for social sciences (SPSS) version 22. Qualitative data from interviews were analyzed thematically. The study revealed that cognitive engagement was a significant predictor of academic achievement among secondary school students studied (r=.376, N=312, p =.01. The study recommended that school based teacher counsellors should utilize cognitive behavioural therapy techniques during counselling sessions with students in school in order to enhance cognitive engagement.