In this study, we compared the effects of cooperative flipped learning (CFL) on science achievement and learning motivation with those of simple flipped learning (SFL) and traditional lecture (TL) using a mixed-methods design. Three classes containing a total of 65 first-year high school students in South Korea were randomly assigned to the CFL, SFL, and TL conditions and taught the chemistry content of an Integrated Science curriculum in 12 lessons over about 4 weeks. In our research design, we paid particular attention to controlling the overall learning time in both the pre- and in-class contexts of the three groups. Our quantitative analysis confirmed that CFL positively affected motivation, but it negatively affected achievement. SFL showed the opposite results. In qualitative analysis, video watching in FL was rated satisfactorily in most cases, but some students reported that they lacked time. CFL inherited both the pros and cons of cooperative learning with regard to in-class interaction, and the effects of SFL depended on individual students' learning abilities. As a consequence, the balance between pre- and in-class learning should be considered carefully when implementing FL, and lab sessions are suitable candidates for this instructional system.