The Republic has inherited a developed education system from the Soviet Union and access to pre-primary, primary and secondary education remains moderately high, although indicators have shown a downward trend since the early 1990s. The slowdown of the Kyrgyz economy in the 1990s has had a negative impact on all education sub-sectors (UNESCO 2008). Access to pre-primary education has experienced exceptional setbacks when the majority of public ECD establishments were sold off for private and commercial use (IBE 2011). In remote rural areas, access to primary and secondary schooling is also a challenge. In fact, extreme rural poverty forces many children to start working at a very young age and abandon their studies in primary schools. The net enrolment rate for first year of primary education was at 60.7% in 2006/7. However, independent studies have suggested that these official statistics over-represent school attendance by 6 times. The rate of enrolment dramatically drops with age in rural areas (UNESCO 2008). The stark regional differences in terms of access to all levels of education are the main pressing challenge faced by the education system in Kyrgyzstan. In addition, there are disparities between the Russian and Kyrgyz students at the level of higher education: the majority of the former attend HEIs while the latter attend an array of TVET programmes.

Kyrgyzstan inherited high-quality primary and secondary education from the Soviet Union. However, UNESCO and UNICEF funded studies in 2001 and 2005 have demonstrated a general downward trend in the quality, particularly that of primary education in the Republic. This trend has been attributed to two main factors. Firstly, pre-primary education is not compulsory in Kyrgyzstan. Therefore, the majority of children who start primary school are unprepared for learning in school. Secondly, at the primary and secondary school levels, curricula are overcrowded with too many subjects, and textbooks are often out-of-date and not easily accessible (UNESCO 2008). The vast disparities between rural and urban areas affect the overall quality of education and achievement. Finally, low teacher salaries in the public education system and the perceived lacking of prestige of teaching profession have been attracting fewer qualified candidates, thus negatively affecting the quality of teaching and learning. 

The MoES is responsible for financing higher and secondary professional education as well as boarding schools for children with special needs and for gifted children. The funding for primary and secondary schooling is a local responsibility. Initially, the education sector was intended to receive the largest share of funding from state budget of Kyrgyzstan. However, since independence other social problems have been taking precedence, leading to a noticeable reduction of funding for education. In 2008, public expenditure on education represented 5.9% of GDP and 19% of total government expenditures. In Kyrgyzstan, inequalities in school financing mirror the rural-urban divide. Primary and secondary schools in Bishkek build up their budgets by charging fees for enrolment and other additional services (UNESCO 2008). On average, 35% of school expenditures of primary schools in urban areas and 25% in rural areas come from non-budget areas, making it even more challenging for the rural poor to access education (UNICEF n.d.(a)).

The Kyrgyz national government is seeking to address the following major problems related to management, quality and access of education in the country. The basic objective of MoES is to introduce a modern school management system that facilitates economic growth. However, the capacity to collect and analyse data necessary for such modernization is limited even at the national level. The Ministry also suffers from inadequate budget that permits only a minimum number of analysts to be employed. In terms of quality, the Country Development Strategy (CDS) of 2009-2011 identified several areas that require immediate attention. They include: development of state education standards by creating the Framework National Curriculum; improving education programmes and content; forming an independent assessment and control system, etc. National capacities to provide well-funded, modern training programmes for teachers are also limited. Secondary schools still suffer from insufficient financing for learning materials. The CDS document recognizes the need to improve the training structure of education personnel across the board. The one inherent challenge of the Kyrgyz education system is the growing gap between rural and urban populations. This disparity is a cross-cutting issue that affects all of the education levels in Kyrgyzstan and is detrimental to the course of development and economic growth of the nation (Government of Kyrgyzstan 2006).