Building an inclusive education system is necessary to realize a symbiotic society, and the promotion of exchange and joint learning is one of the key elements of this system. Until now, there are only a few reports on “Exchange and Joint Learning” at the high school level, and most of them are conducted through events and club activities among schools established in the same school district. This study examined attitudinal changes in the teachers and students of the two schools based on three years of exchange and joint learning practice during the “Period for Inquiry-Based Cross-Disciplinary Study” at the upper secondary school level, transcending the administrative boundaries of prefectural and municipal governments. Through continuous efforts, the sense of resistance between the two schools was reduced, teachers’ cooperation was strengthened, and students got to know and understand each other. The characteristics of the “Period for Inquiry-Based Cross-Disciplinary Study” may be a reason for facilitating exchange and collaborative learning. To sustain exchange and collaborative learning, it is considered important to place it in the curricula of both schools and to evaluate and improve it after implementation intentionally.