The purpose of the study was to investigate the analysis of school-based instructional supervision in primary schools in Niger State, Nigeria It was guided by six objectives; among which are to Determine the analysis of Head teachers' checking of teachers' record of work, examine the Head teachers' classroom visit, determine the Head teachers' checking of pupils' exercise books among others. The researcher applied descriptive survey research design in the study. The population of the study comprised 371 primary schools in Niger State. The sample was made up of 80 Head teachers,114 teachers,12 Supervisors and 40 PTA officials from the selected Education Authority relying on research advisor sample size table(2006). The instrument for data collection was Analysis of School Based Instructional Supervision on Primary School Pupils Academic Performance Questionnaire. Six research questions were asked and formulated. The research questions were answered using mean and standard deviation. The major findings showed that Head teachers' instructional supervision on checking of teachers' records of Work has motivated teachers' to keep up to date record of work in primary schools, Head teachers' classroom visit has great influence on pupils' academic performance. Pupils' academic performance has a link with head teachers' checking of pupils' exercise books. The opinions of respondents on the analysis of head teachers' evaluation of scheme of work on pupils' academic performance, Opinions regarding classroom visits, checking of pupils' exercise books, assessing of teachers' lesson plan/note among others, did not differ significantly. Also, based on the findings ,it was recommended that every head teacher should make it a point of duty to regularly evaluate scheme of work. This will keep them abreast of their responsibilities at all time. For effective school based instructional supervision, head teachers should as a matter of importance ensure classroom visit regularly. The checking of pupil exercise books should be a regular activity by the head teachers; this will make both teachers and pupils to sit- up properly.