The aim of the study was to analyse the effect of school management mechanisms on the discipline of pupils in upper basic primary level. This study examined the effect of; (a) guidance and counselling on the discipline of pupils, (b) school-rules and regulations on the discipline of pupils, and (c) school-family initiative program on the discipline of pupils in upper primary basic level. A cross sectional survey design using both quantitative and qualitative approaches was adopted to obtain data from a sample of 291 participants from 11 primary schools. Both the Statistical Package for Social Sciences (SPSS) and thematic content analysis for quantitative and qualitative data analysis respectively, were used. The effect results highlighted by the multiple regression for guidance and counselling and discipline were; r = 0.628; p-value, 0.003 < 0.05; 95%, school rules and regulations and discipline were; r = 0.671; p-value, 0.009 < 0.05; 95%, and school-family initiative and discipline were; r = 0.601; p-value, 0.004 < 0.05; 95%. It was concluded that guidance and counselling, school rules and regulation, and school-family initiative were significant predictors of pupils' discipline in upper primary basic level. It is recommended that school management should be committed in executing school management mechanisms in their hierarchy of importance to effectively implement discipline in upper primary basic level.