Junior school learners are reaching the final stage of lower secondary education with serious gaps in reading and numeracy, leaving many without the basic skills needed to cope with senior school, a new nationwide study has found.
The report by Usawa Agenda shows that 29 per cent of Grade 9 learners have not acquired both foundational literacy and numeracy competencies expected at that stage.
The situation is worse in public and rural schools, where learners continue to perform below those in private and urban institutions.
The findings are contained in the 2026 Status of Junior School Education Report, which examined the state of junior school education across the country and highlighted weaknesses affecting learners, teachers and schools.
The study covered all 47 counties and involved 41,156 households, 1,527 schools and 49,835 learners. It also included refugee communities in Dadaab, Kakuma and Kalobeyei.
The report found that the problem is not new among Grade 9 learners but starts much earlier in the education system. At Grade 7, 41 per cent of learners lack both literacy and numeracy competencies.
Although the number improves as learners move through junior school, the gains are not enough to ensure that all learners leave Grade 9 with the required basic skills.
One in five Grade 9 learners cannot read a Grade 3 English story, while three in 10 learners in Grade 7 struggle with the same task.
"A substantial share of learners have progressed through junior school without mastering the foundational literacy and numeracy competencies that the curriculum assumes they have already acquired" notes the report.
The findings come at a critical point because junior school, covering Grades 7, 8 and 9, is expected to prepare learners for senior school under the competency-based education system.
Learners at this level are expected to build on skills developed in the early years while gaining wider knowledge and identifying their interests, talents and possible education pathways.
However, the report found that the schools themselves do not have equal capacity to provide this support.
Only 27.5 per cent of junior schools have functional science laboratories, while 27 per cent have libraries. A further 34.3 per cent have adequate learning materials and only 46.3 per cent have computers for learners.
The differences become more visible when schools are compared by region.
Nairobi City County has functional science laboratories in 98.7 per cent of its junior schools, while the proportion falls to 15.4 per cent in North Eastern and 13.8 per cent in Western.
Private schools and those located in urban areas were generally found to have better facilities and resources than public and rural schools.
Teacher availability and distribution also remain uneven. Social sciences teachers make up 58.5 per cent of the teaching workforce in junior schools, while STEM teachers account for 33.1 per cent. Those specialising in arts and sports represent only 8.4 per cent.
The report also points to delays in school funding as another issue affecting education delivery. Only 52.3 per cent of junior schools receive financial disbursements on time.
The cost of entering junior school places another burden on families, with expenses varying according to whether learners attend public or private schools and whether the schools are located in rural or urban areas.
The estimated entry cost for a learner in a rural public school is Sh8,186, compared with Sh11,362 in an urban public school.
For private schools, the estimated cost is Sh22,223 in rural areas and Sh21,954 in urban areas. According to the report, fees account for the biggest share of these costs.
Usawa Agenda Executive Director Emmanuel Manyasa said schools were facing difficulties in keeping learners in class while also supporting their learning.
"I think there are challenges keeping learners in school, managing them and handling their learning. The challenge is that schools themselves are facing challenges in preparing learners for senior school," said Usawa Agenda Executive Director Emmanuel Manyasa.
The report found that access to junior school is almost evenly divided between boys and girls. Girls make up 49.3 per cent of enrolment nationally, while boys account for 50.7 per cent.
Attendance, however, is a major concern in some communities. Refugee community schools record an absenteeism rate of 13.4 per cent, compared with 5.3 per cent in public schools and 3.3 per cent in private schools.
The study identifies children with disabilities, learners in rural and public schools, those living in Arid and Semi-Arid Land counties and learners in refugee communities among those facing several barriers at the same time.
Boys also tend to record weaker results in literacy and numeracy compared with girls.
The report says what happens at home and before a child enters school can also shape learning outcomes. Learners who attend pre-primary education have an early advantage, while mothers' education, help with homework and household wealth are linked to better chances of developing basic literacy and numeracy skills.
Hellen Avisa, director of the Directorate of Junior School at the Ministry of Education, said the country needs to address the problem before learning gaps become harder to correct.
"When a child has good foundational skills, they manage to read and solve a few problems. When there is poor foundational skills lacquisition], starting from the ECD or early learning level, it becomes an issue. Those children grow up, and it becomes difficult. As partners, as a ministry, we need to put our heads together and see how can this happen under our watch," said Hellen Avisa, director of the Directorate of Junior School at the Ministry of Education.
Avisa represented Principal Secretary John Olooltua during the report launch.
She said the findings should be used to guide practical measures in schools and at national and county levels.
"The findings presented today provide more than a snapshot of our education system. They provide an opportunity for reflection and action. When we have evidence, what next? We need to act, so evidence must inform action. The findings should help us identify the areas requiring attention at national, county, and school levels. Where the evidence points to gaps, we must ask, what practical interventions are necessary and who should take responsibility?" she said.
The report places the learning problem within five broad areas: participation and attendance, school readiness and affordability, school leadership and staffing, learning outcomes, and equity.
It says government efforts have helped increase the number of children entering classrooms but have not fully solved the question of whether learners are acquiring the skills they need.
"The evidence shows that the government policies have succeeded in bringing learners into classrooms but have not yet succeeded in ensuring that they learn or that the schools they enter are equally equipped to teach them," reads part of the report.
The study further says learning is affected by a combination of school and home conditions. A child's experiences before joining school, the quality of the learning environment and the support available at home all contribute to their progress.
With nearly three in 10 learners still lacking combined literacy and numeracy competencies by the end of Grade 9, the report raises questions about whether junior schools are giving all learners an equal foundation as they prepare to enter senior school.