The focus of the study is on disparities in enrolment and attendance between males and females in basic schools in the Northern Region of Ghana. The literature reviewed showed that factors such as high cost of education, household chores, household resources and government subsidy on education militate against the participation of females in basic education. Also, cultural factors which include fostering, child betrothal and religion in some cases as well as school-based factors such as teacher absenteeism, lack of female teachers as role models are responsible for the females? inability to participate effectively in basic education. Gender was virtually ignored in most of these studies. This study investigated how the socio-economic, cultural and school-based factors as well as the collaboration between GES and the NGOs affected and created disparity in school enrolment and attendance either in favour of the males or females in basic schools in the Northern Region of Ghana. Multi-stage cluster sampling technique was used to select the respondents and both questionnaires and interview guides were used for the data collection. The data was processed with the Statistiscal Package for Social Scientists and percentages. Charts, cross-tabulation and regression were used for the analyses of the quantitative data while the qualitative data was used to support and explain the quantitative data, except instances where some variables emerged in the course of the interviews. These variables were analysed thematically. The study found that socio-economic factors such as households? income, resources, household chores, market days and cost associated with schooling have affected females? enrolment and attendance more than males. The preference for males and the belief that investing in females? education means investing in the prospective husbands accounted for the disparity in enrolment and attendance. The cost of educating the female child per annum was higher than the cost of educating the male child (GHc 81.3 and GHc 69.9 respectively) due to the fact that female needs such as school uniform, books, “chop” money to effectively participate in education were more when compared to males and this created disparity in enrolment and attendance in many schools. The levels at which parents acquired education in the region does not determine the levels at which their children acquire education. Pupils in basic schools were not enrolled because their parents? have attained higher levels of education. Polygyny, early marriage, fostering, menstruation, festivals and funeral rites affected disparity in attendance in favour of males because of the negative perceptions of households about females?education. Large class size, teacher absenteeism in many instances discouraged females from attending school more than males. The School Feeding Programme and the Capitation Grant positively affected the enrolment of females more than males. Capitation Grant does not affect school attendance in the region because there was no evidence in the schools or from GES to show this. While the Gender Parity Indices in enrolment favoured the females, the indices in school attendance favoured the males in the region. NGOs have collaborated with GES in research, provision of incentives to girls, training of the personnel of GES, advocacy, scholarships and formation of girls clubs in schools but lack of trust and effective preservation of data as well disparity in enrolment at the start of school cycle by many schools accounted for the continued disparity in enrolment between males and females. A policy review to include all the stakeholders in basic education (parents, teachers, pupils? and NGOs) is necessary else, a key target of the Millennium Development Goals which aims at achieving parity at the basic school level will remain an illusion and a “wild goose chase.”