The study examined the effect of virtual learning on academic performance, autonomy and response rate of Basic Science students in JSS 2 in Ojo Local Government Area of Lagos State. Two hypotheses were tested using pre-test post-test non-equivalent quasi-experimental design. Simple random sampling technique was used to select 90 JSS 2 students from Junior Secondary Schools in Ojo Local Government Area from. A self-designed multiple-choice Achievement Test in Basic Science (ATBS) which measures the academic performance, response rate and autonomy of the students with 30 items was used for data collection. The instrument was tested for item difficulty index, discrimination index. The Kuder Richardson (KR-20) value was 0.78. The item was reduced to 20 items after the item analysis. The outcome of the analyses revealed that students taught using VLE outperformed those taught using the CLE. Based on the findings, It was recommended that all schools should introduce virtual learning classrooms to ensure a continuous interaction of the learners anywhere-anyplace with each other, the content and the instructor or teacher.