Recent education roles encourage willingness to learn individually, solve unfamiliar problems using knowledge acquired through information and communication technologies (ICTs), and collaborate with others. Various learning methods to cultivate this ability have been invented and researchers discussed learning effect on such methods with qualitative and quantitative analyses. One of the authors introduced pair programming as a method of peer learning and flip teaching, which consists of preliminary learning of basic programming and advanced learning practices based on peer activity in classroom lessons, into computer simulation practices for undergraduate students. With introducing class schedule design for flip teaching and development of peer learning preparation support system for determining the appropriate pair formation and seat allocation in the classroom utilizing a probabilistic combinatorial optimization algorithm, this study focuses on learning behavior of wellperforming students, analyzing learning records and access logs on a learning management system and answers to a questionnaire administered after the practices. In this analysis, we attempted to discriminate behavior of well-performing students observed from the learning records, access logs, and questionnaire to discover best practices for improving the performance of medium to bottom-line students. Well-performing students tended to prepare for classroom lessons in good time, but their performance depended on the lesson content difficulty. A correlation was observed between the frequency of interaction among students and skill acquisition. We discuss how to improve learning environments using ICTs and collaborative learning methods based on the analysis.