This study assessed classroom management variables and primary school system effectiveness in Calabar-South Local Government Area of Cross River State. Three null hypotheses were formulated to direct the study. The ex-post facto research design was adopted for the study. Census technique was employed in selecting the entire population of 525 academic staff (21 head teachers, 21 deputy head teachers, and 483 teachers) distributed across 21 public primary schools in the area of study. “Classroom Management Variables and School Effectiveness Questionnaire (CMVSEQ) was the instrument used for data collection, with reliability estimates which ranged from .86 and .91 that were obtained through Cronbach Alpha technique. Collected data were analyzed using descriptive statistics, while the null hypotheses were all tested at .05 level of significance using Pearson Product Moment Correlation and One-Way ANOVA where applicable. Findings from the study revealed that public primary school system effectiveness in the area of study, was generally low; there is a significant relationship between classroom coordination and primary school system effectiveness; there is a significant influence of class size and classroom learning environment respectively, on primary school system effectiveness. Based on the findings, it was recommended amongst others that teachers be retrained in terms of classroom coordination and management, to enable them to acquire new techniques of classroom management, as well as the modification or elimination of obsolete ones