Republic of Indonesia is the largest archipelagic and Muslim majority country in the world comprising of various small and big islands. Almost 300 languages are spoken in the country, but Indonesians believe in ‘Benika Tungal Ika’ mean diversity is strength. Indonesian Islamic education system covets overall development of students’ personality including the religious, cognitive, physical, emotional, physical and scientific aspects. This paper aims to explore the perceptions of alumni about contribution of Sekola Islam, Pesantren and Pandok in nation building of Indonesia. Paper is based on qualitative analysis of data collected through semi structured interviews with alumni of Sekola Islam, Pesantrens and Pandok. The results showed that Pesantrens, Sekola Islam and Pandok network of Islamic Education Institutions is root of education system and has played a significant role in nation building of Indonesia. Islamic Education Institutions have contributed for the religious, societal, economic and technological development of Indonesia and produced renowned leaders in the field of politics, religion and education.