The study examined the effect of Quality Assurance on the Effectiveness of Lagos State Junior Secondary Schools. The factors of effectiveness that were considered included teachers’ input, school leadership and learning environment. A stratified sample of 30 schools was selected from a population of 313 from the six Education Districts of the state on an equal basis of five schools from each district. From each of the sample schools were also selected 30 teachers, again on stratification based on gender, qualification and experience. A questionnaire was designed for the study to collect pertinent data 900 copies of which were administered but 868 or 96.4% of which were returned. The questionnaire was subjected to a test of face validity and test-retest reliability. The reliability coefficient was found to be 0.76. The collected data were then subjected to chi -square analysis and in accordance with the hypotheses generated to guide the study. Results of the analyses indicate that quality assurance has a significant effect on each of teachers’ input and school leadership but not on learning environment. Based on the findings, recommendations were made to the effect that quality assurance should be intensified and possibly private participation in the practice should be encouraged.