This study aims to investigate the challenges of developing character education based on Islamic pluralism in the curriculum of Modern Islamic Boarding Schools in the Pandemic era. The research location is the modern Islamic boarding school Gontor in East Java Province. The qualitative research design with a phenomenological approach examines five central aspects of character education development based on Islamic pluralism: religiosity, independence, integrity, mutual cooperation, and nationalism. The findings reveal that the primary challenge in developing character education is the lecturers' unequal ability to develop an effective character education curriculum. Not all lecturers have qualified competencies to integrate character values into their teaching subjects. Studies have yet to address character values in the curriculum in the learning process. Meanwhile, external challenges minimally affect the development of character education because the modern Islamic boarding school in Gontor has five aspects of character education development strongly supporting the modern "pesantren" curriculum. The readiness of the "pesantren" curriculum can form a strong character to face challenges. "Pesantren" involves aspects of knowledge and habit, continuously practiced while maintaining the health protocols recommended by the government. The expected implication is that stakeholders consistently provide intervention and reinforcement in the long term. Thus, character education based on Nusantara Islamic Pluralism in modern Islamic boarding schools can realize the ideals of the goals of national education and benefit humanity.