Nyeri children are the best in reading and mathematics, a report by an education lobby shows.
Pupils in Nairobi and Kajiado are in second and third positions respectively.
The findings of a survey by Uwezo Kenya shows that more than 50 per cent of Class Three pupils in these regions can do Standard Two work.
The report also shows that although 58 per cent of pupils in Nyeri have strong English reading skills and are good at solving division problems in mathematics, their general performance is still poor.
The document says absenteeism among primary school teachers and pupils in the country had dropped from 16 to 12 per cent nationally.
Murang'a County had the lowest number of children out of school. One out of 100 children failed to attend school.
Most of the children out of school are in arid and semi-arid counties such as Baringo and West Pokot, and urban areas with large slum populations, including Nairobi North.
"The gap in student attendance can be attributed to the inequitable distribution of resources, which posed as a challenge, especially in arid and semi-arid areas. Arid districts have much lower learning levels than urban and agriculturally rich rural districts," says the report.
Further, the number of children aged three to five attending pre-school has increased by 13 per cent since 2011.
Kisii was the best performing county for pre-school pupils. The children are aged between three and five.
However, 15 per cent of five-year-olds attend primary school prematurely. According to the report, most of the underage children go to public primary schools.
According to the survey, late enrolment and repeating contribute to the high number of overage children in upper classes. Lower primary school has more underage children while higher classes have more overage children.
"Two out of 10 pupils in classes Two to Four are underage while almost half of those in classes Five to Eight are overage. Class Seven has the highest number of overage children, at 49 per cent," says the report.
At the same time, 18 per cent of Standard Three pupils in Marsabit County can hardly tackle Standard Two class work.
The learning assessment report says the pupils have challenges in communicating in either English or Kiswahili.
According to the document, in mathematics, the pupils perform poorly in the section involving division.
The study, which was launched at St Stephen's ACK Conference Hall in Marsabit, says the enrolment of children and school attendance are below the national average.
However, the teacher daily attendance rate is slightly higher than the national average.
Marsabit was ranked position 38 out of 47 counties in the lobby's study.
Deputy Governor Omar Ali Abdi, who presided over the launch of the report, said Marsabit's harsh climatic conditions were a major drawback in efforts to improve education in the county.