This study analysed the modalities and roles of pesantren (Islamic Boarding Schools) to face the issues of terrorism in the region of Malang. Contrary to the notion which stated that pesantren are the headquarters of terrorist groups, this paper discusses the existence of pesantren in the region of Malang with a various ideological background as the strategic and prominent stakeholders to face the issues of terrorism. The methodology was descriptive, with the concept of modality for deradicalisation. The result found that pesantren have modalities in dealing with issues of terrorism, namely, the spiritual modalities, the curriculum modality, the kyai and santri relations modality, and the social modality. Moreover, it is indicated that the pesantren and issues of terrorism are not interrelated. Pesantren have created an education system as the internal and external roles that can overcome the spread of radical movement activities and the issues of terrorism.