One of the most difficult and unresolved issue in northern Nigerian and Nigeria in general is the Almajiri and Almajirci System of Education. The system which rooted in traditional Islamic learning faces significant challenges including poor funding, lack of infrastructure, inadequate teacher training and the children’s vulnerability to exploitation of hardship and the children’s limited access to basic needs like food, shelter and parental care. The Federal Government has made an effort to Integrate two Educational Systems and built modern Qur’anic primary Schools in Northern parts of Nigerian in which Six of their types were located at Damaturu, Geidam, Gashua, Nguru, Damagun and Buni Yadi of Yobe state, from among these six, only two of them are in existence while the remaining four are either dilapidated (decay) or being used by soldiers to counter insurgency. Even the two that were functioning, it is not in accordance with the purpose of their establishment the schools are operating in two different sessions, i.e Morning and afternoon. The morning session is for Western Education while the Evening session is for qur’anic lessons. And another method of the operation is that the Schools are Day only Schools (not boarding). This clearly shows that the aim of the integration of the two different system of Education has been defeated, since they are supposed to be concurrently operating. Another major problem faced by the Integration is lack of awareness and sensitization from the part of the Government to the targeted populace.