Mbooni Boys, Makueni Girls, Mwaani Boys, Kalulini Boys and St Josep’s Girls High school are among the best Extra County schools in Makueni County.
Extra County Schools in Kenya form the second tier of secondary schools; after National schools. They were formerly referred to as Provincial schools. These schools are distributed all over the Country with each county having its share. The schools admit students from all over the country. These schools are in 3 Categories i.e category 1 (C1), Category 2 (C2) and Category 3 (C3). The Schools are either of Mixed or single sex type.
Here are the Extra County Schools in Makueni County:
| School Code | School Name | Category | Type | Cluster |
| 18307102 | MAKUENI GIRLS HIGH SCHOOL | Extra County | Girls | C1 |
| 18307103 | MWAANI GIRLS SECONDARY SCHOOL | Extra County | Girls | C3 |
| 18307105 | MWAANI BOYS’ SECONDARY SCHOOL | Extra County | Boys | C1 |
| 18307201 | KAUMONI BOYS SECONDARY SCHOOL | Extra County | Boys | C1 |
| 18323102 | MBOONI BOYS HIGH SCHOOL | Extra County | Boys | C1 |
| 18324205 | NGOTO BOYS HIGH SCHOOL | Extra County | Boys | C1 |
| 18324206 | BARAZANI GIRLS’ HIGH SCHOOL | Extra County | Girls | C1 |
| 18324301 | MATILIKU SECONDARY SCHOOL | Extra County | Boys | C3 |
| 18325201 | KALULINI BOYS’ HIGH SCHOOL | Extra County | Boys | C1 |
| 18325209 | ST. JOSEPH’S GIRLS SECONDARY KIBWEZI | Extra County | Girls | C1 |
| 18335201 | ST. MARTIN KATHONZWENI SCHOOL | Extra County | Boys | C2 |
| 18336101 | PRECIOUS BLOOD SECONDARY SCHOOL – KILUNGU | Extra County | Girls | C1 |
| 18346101 | KITONDO SECONDARY SCHOOL | Extra County | Boys | C1 |
| 18346102 | KISAU GIRLS SECONDARY SCHOOL | Extra County | Girls | C1 |
| 18346205 | KALAWA SECONDARY SCHOOL | Extra County | Boys | C1 |
| 18347401 | KASIKEU SECONDARY SCHOOL | Extra County | Boys | C3 |
| 18347501 | MUKAA BOYS’ HIGH SCHOOL | Extra County | Boys | C1 |
| 18348101 | MAKINDU SECONDARY SCHOOL | Extra County | Boys | C1 |
| 18348112 | MOI GIRLS SECONDARY SCHOOL – KIBWEZI | Extra County | Girls | C3 |
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