The researcher was prompted to carry out this study because of the concerns raised by educationists, parents, teachers and other lay people over the persistent poor performance in K.C.S.E. examinations, particularly in Bureti District secondary schools. The primary purpose of this study was to investigate the effectiveness of secondary school   headteachers instructional supervision on academic achievements in secondary schools since academic success or failure of the school rests on the managerial capability of   headteachers. It was the researcher‟s view that the study would go a long way in identifying deficiencies hindering effective supervision and making appropriate recommendations geared towards the improvement of instructional supervision among the headteachers in secondary schools. The study employed a descriptive research design to investigate the effect of supervision on academic achievement by headteachers. The population of the study comprised of all the 30 secondary schools in Roret and Bureti Divisions of Bureti District. From this, 10 schools were sampled through simple random sampling procedure. Each headteacher and four teachers from the 10 schools were given questionnaires to fill on the effectiveness of   headteachers in instructional supervision to establish if this led to academic achievement. The questionnaires were developed by the researcher guided by the supervisors. The data collected from the questionnaires were analyzed manually, using a calculator where the researcher put similar comments in categories and drew frequency and distribution tables to establish the effectiveness of headteachers in instructional supervision on academic achievement in secondary schools in Roret and Bureti divisions of Bureti District. The findings of the study were discussed by focusing on effectiveness of headteachers‟ instructional supervision on academic achievement in the selected secondary schools in Roret and Bureti division. The study found out that 6 headteachers (60%) in secondary schools in Bureti District did not carry out effective instructional supervision and that only 2 Heads of Departments out of 6 (33.3%) were involved in the process of instructional supervision through delegation by headteachers. It was concluded that since most headteachers in Bureti District secondary schools did not carry out effective instructional supervision, the trend had contributed to lower performance in K.C.S.E examinations in the district. It was recommended that headteachers be re-trained on roles of effective instructional supervision on academic achievement. It was also recommended that headteachers should involve heads of departments in instructional supervision through effective delegation of duties.