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County secondary schools in Kenya form the third tier after national and extra-county schools respectively.
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Most of Kenyan learners are absorbed by these schools.
Admission to county schools is made online by the Ministry of Education.
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They are either mixed or single-sex.
Here is a list of County Schools in Mombasa County:
| NAME | KNEC CODE | TYPE | CATEGORY | |
| 1 | ALLIDINA VISRAM HIGH SCHOOL | 03106101 | Boys | County |
| 2 | TUDOR DAY SECONDARY SCHOOL | 03106103 | Boys | County |
| 3 | STAR OF THE SEA HIGH SCHOOL | 03106105 | Girls | County |
| 4 | SACRED HEART HIGH SCHOOL, MOMBASA | 03106107 | Mixed | County |
| 5 | SERANI SECONDARY SCHOOL | 03106116 | Boys | County |
| 6 | SHARIFF NASSIR GIRLS | 03106118 | Girls | County |
| 7 | MBARAKI GIRLS SECONDARY SCHOOL | 03106121 | Girls | County |
| 8 | TONONOKA SECONDARY SCHOOL | 03106122 | Boys | County |
| 9 | ALFARSY GIRLS SECONDARY SCHOOL | 03106124 | Girls | County |
| 10 | MVITA BOYS SECONDARY SCHOOL | 03106125 | Boys | County |
| 11 | MAKANDE GIRLS SECONDARY SCHOOL | 03106132 | Girls | County |
| 12 | MAKUPA BOYS SECONDARY SCHOOL | 03106133 | Boys | County |
| 13 | MOI FORCES ACADEMY-MOMBASA | 03108101 | Mixed | County |
| 14 | MTONGWE GIRLS SECONDARY SCHOOL | 03108103 | Girls | County |
| 15 | SHIKAADABU SECONDARY SCHOOL | 03108104 | Mixed | County |
| 16 | MWAHIMA SECONDARY SCHOOL | 03108114 | Mixed | County |
| 17 | LIKONI SECONDARY SCHOOL | 03108201 | Boys | County |
| 18 | PUMA SECONDARY SCHOOL | 03108209 | Mixed | County |
| 19 | MRIMA MIXED DAY SECONDARY SCHOOL | 03108211 | Mixed | County |
| 20 | BUBUBU BOYS SECONDARY SCHOOL | 03108217 | Boys | County |
| 21 | CHANGAMWE SECONDARY SCHOOL | 03120101 | Mixed | County |
| 22 | ST. CHARLES LWANGA SECONDARY SCHOOL | 03120102 | Mixed | County |
| 23 | MWIJABU SECONDARY SCHOOL | 03120117 | Mixed | County |
| 24 | CHAANI SECONDARY SCHOOL | 03120118 | Mixed | County |
| 25 | BOMU SECONDARY SCHOOL | 03120121 | Mixed | County |
| 26 | MWAKIRUNGE SECONDARY SCHOOL | 03121204 | Mixed | County |
| 27 | MTOPANGA MIXED SECONDARY SCHOOL | 03121216 | Mixed | County |
| 28 | HASSAN JOHO GIRLS’ SECONDARY SCHOOL | 03121220 | Girls | County |
| 29 | MARIMANI MIXED SECONDARY SCHOOL | 03121226 | Mixed | County |
| 30 | KAJEMBE HIGH SCHOOL | 03124105 | Mixed | County |
| 31 | MIRITINI SECONDARY SCHOOL | 03124108 | Mixed | County |
| 32 | JOMVU GIRLS HIGH SCHOOL | 03124110 | Girls | County |
| 33 | MIRITINI COMPLEX HIGH SCHOOL | 03124111 | Mixed | County |
| 34 | MAWENI MIXED SECONDARY SCHOOL | 03126106 | Mixed | County |
| 35 | FRERETOWN SECONDARY SCHOOL | 03126123 | Mixed | County |
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