This study delves into the transformations within the Islamic Boarding School (Pesantren) education system over time and their implications for the learning methods employed by students. Guided by a case study research design with a descriptive qualitative approach, this research focuses on two of the oldest Islamic boarding schools: Tegalsari Ponorogo Islamic Boarding School and Jamsaren Solo Islamic Boarding School. Key participants, comprising leaders and administrators well-versed in the history and evolution of pesantren education and learning systems since their inception, serve as the primary data sources. The findings are structured into three parts. The initial segment unveils that Tegalsari Ponorogo pesantren originally functioned as a center for non-formal education, characteristic of Salafi pesantren. As time progressed, the establishment of Modern Darussalam pesantren introduced contemporary formal education with regular and intensive programs, marking a departure from traditional non-formal education associated with Salafi pesantren. In the second part, the study highlights the evolution of Jamsaren Solo pesantren education, which transitioned from classical education methods to a modern formal education approach employing a classroom system. The third part elucidates that the transformation in pesantren education has contributed to a reduction in the learning gap. Students now acquire not only religious knowledge but also a range of general disciplines, leading to notable achievements. In summary, the educational transformation has impacted the learning system, facilitating the acquisition of knowledge and skills relevant to contemporary times. The study underscores the need for collaboration between the government and pesantren leaders to fortify the pesantren education system. This collaboration aims to cultivate Indonesian pesantren capable of producing young professionals who contribute significantly to the nation, religion, and state.