This research aims to determine the differences in critical thinking skills and cognitive learning outcomes, as well as the responses of students who taking conventional learning and virtual labs on the concept of the human breathing system. The method used is an experimental method by design pretest-posttest control group design. The research population is high school students at class XI in the second semester of school time. Two classes with 25 students each were chosen purposively for experiment and control class. The experimental classed was taught by using learning media of virtual laboratory software, while the control class was taught with conventional learning and both classes were applied the Direct Instruction Model. Pretest and posttest on critical thinking skills and cognitive learning outcomes of the students in both classes were compared and analyzed by using a test; essay and multiple-choice performed with t-test (Independent Samples t-Test). The research results shows that students at experimental class have significantly higher posttest scores than the their peers in control class with p < 0.05. Majority students gave 94.8% of positive responds on the using of virtual laboratory software for the learning media of human breathing system.