Pondok Pesantren was an Indigenous Cultura, which is it is a phenomenon which is unique and has unique existence and role in the history of the Indonesian nation. Its existence has no more but first before the establishment of the Republic of Indonesia. Initially, Pondok Pesantren is broadcasting institutions and the Islamic-based society, but in line with the changes and dynamics that develop in the middle of the community, it was charged must be able to become a bridge for the transformation of socio-cultural community where it is in all areas of life.
 
Therefore, Drs. KH.Mahrus Amin, Chairman of the Education and Endowments of Annajah Islamiyah  Foundation Jakarta, Pondok Pesantren Madinatunnajah established on 14 February 1997, conducted by the opening of the deceased KH. Shoiman Luqmanul Hakim, one of the leaders Pondok Modern Gontor, Ponorogo. In further developments, Pondok Pesantren Madinatunnajah in the process of education, which held for 24 hours referred to the Life Skills Education. With this approach, we expected to appear some cadres and the people who came from various regions of the country.
 
And so far, the students comes from some provinces, from Flores, Maluku, South Sulawesi, South Sumatra, Bengkulu, Papua and others, especially those who come from poor families and orphans. For that purpose,  has stood Qur'an Education for Kindergarten Students (TPA), Preschool (Kindergarten), Integrated Madrasah Ibtidaiyah (MIT), Tarbiyatul Mu'allimin wal Mu'allimat (TMI), Ma'had 'Aly / High School Science Tarbiyah. With the number of 376 santri and built by 77 teachers.




1. Preparing cadres of prospective community leaders and the people who faithfully in God, intelligent, strong, skilled and dicipline.

2. Making Pondok Pesantren as educational institutions that have a competitive advantage in the field of science and technology.