On November 22th, 2014, the Education Minister of Japan proposed to promote "active learning" in elementary and secondary education, with the purpose of enabling students study actively and cooperatively to find and solve problems in the society and daily life. Flipped learning is a blending of direct instruction with cooperative "active" learning. Students study basic concepts and principles at home via instructional videos, and they learn in a group to solve problems or co-create knowledge in class. Thus, flipped learning requires students to learn autonomously at home, and to learn actively and cooperatively in class. This study purposed to identify the effects of flipped learning on students' knowledge and skills of instructional design for elementary and secondary education. Participants were 67 Japanese third-year university students who participated in an educational technology class. All of the participants were taking pre-service teacher education courses for elementary and secondary education. Results of the study show that flipped learning has a positive effect on pre-service teachers' knowledge, understanding, and skills of instructional design for elementary and secondary education. Results suggest that if students learn individually out of class at their own pace, they could understand what is important in instructional design, and if students learn actively and cooperatively in class with teachers' facilitation, they could enhance their skills of instructional design.