Pesantren as educational institutions, both modern and traditional, at least maintain the uniqueness of pesantren, which any other institution does not own. The uniqueness often makes some people misunderstand that pesantren practise gender inequality where female students are often not allowed to proceed outside the pesantren or only in the domestic area. This research was a qualitative case study taking place at Pondok Pesantren (PP) Aswaja Nusantara in Mlangi, Sleman, Yogyakarta. This study takes the point of view of the kyai (caretaker) of the Pondok, who serves as a policy maker in the institution. The research question in this study was: What is the concept of gender equality in the education system and pesantren culture at PP Siswa Aswaja Nusantara? The results showed that based on the data provided by caregivers, gender equality in PP Aswaja Nusantara was enacted through the culture of the pesantren and the application of the pesantren education system. Equality is the sense of fairness in paying attention to biological factors and circumstances, both men and women. First, equality in PP Aswaja Nusantara does not mean the same between men and women, and this impacts the division of tasks more concerned with individual abilities than gender. Second, in the education system, PP Aswaja Nusantara provides equal opportunities to all male and female students, both internally and externally.