Supervision in schools is worldwide phenomenon. Head teachers’ instructional supervision practices can improve teaching and learning process to achieve quality academic performance. The purpose of the study was to investigate the influence of head teachers’ instructional supervision practices (independent variable) on academic performance in KCPE (dependent variable). The objectives were; to establish the extent to which head teachers’ checking of teachers’ professional documents influence pupils’ KCPE performance, to examine the extent to which headteachers’ observation of teachers’ lessons influence KCPE performance, to determine the extent to which headteachers’ provision of teaching learning resources influence KCPE performance, to examine the extent to which headteachers’ use of staff meetings influence pupils’ KCPE performance and to examine the extent to which headteachers’ checking of teachers’ punctuality influence pupils’ KCPE performance in Lower Yatta Sub-county, Kenya. Goal Setting Theory by Locke and Latham of 1968 guided this study. Descriptive survey design was used. 61 public primary schools, 427 teachers and 1556 standards eight pupils formed the target population. The study sample comprised of 51 schools, 51 headteachers, 194 teachers and 51 pupil focus groups. Instruments used were questionnaires, focus group discussion guide and document analysis guide. Questionnaires were validated by pretesting and expert judgement while reliability was determined using test retest method and value r = 0.8 obtained. Data was analyzed using descriptive statistics that were frequencies, means, deviations and percentages and presented in tables. Findings using chi-square test at alpha value 0.05 level of significance on instructional supervision and pupils’ KCPE performance showed that; there was significant and positive relationship between checking of professional documents and KCPE performance, there was significant and positive relationship between observation of lessons and KCPE performance, there was significant and positive relationship between provision of teaching learning resources and KCPE performance, there was significant and positive relationship between use of staff meetings and KCPE performance, there was significant and positive relationship between punctuality and KCPE performance. All pvalues greater than critical value, null hypotheses were rejected and alternative hypotheses that there was significant relationship adopted. The findings showed that (403.12>critical value) use of staff meetings showed the greatest influence for KCPE examinations. The study revealed that the specific headteachers’ instructional supervision practices were inadequately performed in Lower yatta Sub-county, Kitui. This study recommends headteachers to be equipped with the required supervision knowledge and skills that would lead to improved pupils’ academic achievement. This may be acquired from management training institutions including Kenya Education Management Institute (KEMI) among other institutions.

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