The purpose of this study was therefore to examine the influence of school based quality assurance practices as performed by the head teachers on pupils’ academic performance of pupils in public primary schools in Subukia sub county, Kenya. The study was based on the value added theory and the production function theory of education. Using the ex post facto research design, the study used census methodology to gather data from all the 42 head teachers of public primary schools in subukia Sub County using structured questionnaires. Validity of the instrument was done based on expert judgment from the department of curriculum and education management of Laikipia University for determining face and content validity. The reliability of the instrument was determined through a single test administration by use of the cronbach alpha coefficient of which an alpha coefficient of 0.791 was obtained and considered acceptable. Nominal scale data was analyzed using frequency counts and percentages. Hypotheses were tested at the .05 level of significance using simple regression analysis. The study found a strong positive significant relationship between head teachers’ planning activities r=.573, p=.00<.05, coordinating practices r=618 p=.00<.05, staffing practices r=689 p=.00<.05 and controlling practices r=667 p=.00<.05 and academic performance of pupils in public primary schools in Subukia sub county, Kenya. The head teachers in public primary schools in Subukia should hold meetings as a quality assurance practices as a means of filtering how various schools stakeholders view quality assurance and implement them in the various aspects in the school management. Particularly, the PTA meetings should be used to moderate administrative processes in order to facilitate effective teaching and learning. PTA and educational administrators make concerted efforts initiate and sustain new projects, rehabilitate dilapidated infrastructures and initiate professional development through staff training. The findings of the study will be beneficial to Quality Assurance and Standards policy makers as they will offer useful suggestions on enhancing quality assurance and standards in primary schools for qualitative improvement of basic education in the country in general and Subukia Sub County in particular. Other researchers will also find the study useful as it will add to the body of existing literature in the field of educational quality assurance and standards.