Global consensus on the importance of gender equity in education is perhaps one of the greatest agreements reached in the twentieth century. However, for countries in the sub Saharan African region where disparities of gender are wide and primary education takes priority, secondary education continues to remain in the periphery. As countries make progress towards the attainment of Universal Primary Education (UPE), the concerns for gender equity and equality have become associated with school access and pupil retention. Yet, patterns and trends in school enrollment suggest that disparities of gender are more complex. As lessons are learned from the achievements and challenges of attaining UPE, it is increasingly apparent that gender disparities within education occur in, within and beyond access to schooling. In other words, the challenge of making education gender equal goes beyond school access and school enrollment. Kenya is a signatory to the 1990 Jomtein Declaration on Education For All (EFA). It is also among the few countries in the sub Saharan Africa region with a significantly reduced gender gap in primary and secondary education. This is in tandem with the third of the eight Millennium Development Goals whose aims bear a broad social and economic development agenda. While education equity is important in Kenya and tremendous progress has been made in primary education, beyond the attainment of Universal Primary Education (UPE) there is an even more significant target; gender equity in education both in primary and secondary education by 2015. The attainment of this target requires more than access to schooling and for this reason it poses great challenges to governments and schools. In light of the progress made in Kenya and the need for more equitable education beyond primary education, this study conceives a need for an incisive examination of education equity priority areas in Kenya. The study argues on the need for a shift of concern and debate from primary education to secondary education because the gains of UPE only become meaningful when education equity is secured in secondary education. The study underscores that beyond school access and retention, education output and outcomes need to become prominent variables because they gauge trends and patterns and the quality of gains made where education is claimed to be both accessible and equitable. Using case study method, the study makes a critical interpretation of the schooling experiences, educational choices, preferences and aspirations of girls taking secondary education in single-sex schools in Murang’a district, Kenya. The study shows that girls schooling experiences are not homogenous and that there are contradictions in the ways that girls experience their schooling and make educational choices. It also shows that girls do not necessarily stand good chances with their education simply because they are enrolled in single-sex schools. The study reveals individual subjectivities and schooling culture to be at the centre of the differences between schools and the schooling experiences that girls have. The two have impact on how girls perceive themselves and their abilities, the preferences they nurture and the educational choices they make. The study draws attention to nuances in access and equity within girls’ education. It draws out issues and nuances linked to gender access, equity and equality with respect to school, teacher and subject access. Though the study is not generaliseable, it shows that in contexts where female access and survival is secured, there is need for attention to be paid to the environments that nurture educational choices and preferences so that the high rates in school access become translated into equally high educational output and outcomes.