County Schools in Kenya form the third tier of secondary schools; after National and Extra County schools, respectively. The schools admit students from majorly within the country. Admissions to these schools is done online by the Ministry of Education.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 County Schools in Mombasa County:
| School Code | School Name | Category | Type |
| 03106101 | ALLIDINA VISRAM HIGH SCHOOL | County | Boys |
| 03106103 | TUDOR DAY SECONDARY SCHOOL | County | Boys |
| 03106105 | STAR OF THE SEA HIGH SCHOOL | County | Girls |
| 03106107 | SACRED HEART HIGH SCHOOL, MOMBASA | County | Mixed |
| 03106116 | SERANI SECONDARY SCHOOL | County | Boys |
| 03106118 | SHARIFF NASSIR GIRLS | County | Girls |
| 03106121 | MBARAKI GIRLS SECONDARY SCHOOL | County | Girls |
| 03106122 | TONONOKA SECONDARY SCHOOL | County | Boys |
| 03106124 | ALFARSY GIRLS SECONDARY SCHOOL | County | Girls |
| 03106125 | MVITA BOYS SECONDARY SCHOOL | County | Boys |
| 03106132 | MAKANDE GIRLS SECONDARY SCHOOL | County | Girls |
| 03106133 | MAKUPA BOYS SECONDARY SCHOOL | County | Boys |
| 03108101 | MOI FORCES ACADEMY-MOMBASA | County | Mixed |
| 03108103 | MTONGWE GIRLS SECONDARY SCHOOL | County | Girls |
| 03108104 | SHIKAADABU SECONDARY SCHOOL | County | Mixed |
| 03108114 | MWAHIMA SECONDARY SCHOOL | County | Mixed |
| 03108201 | LIKONI SECONDARY SCHOOL | County | Boys |
| 03108209 | PUMA SECONDARY SCHOOL | County | Mixed |
| 03108211 | MRIMA MIXED DAY SECONDARY SCHOOL | County | Mixed |
| 03108217 | BUBUBU BOYS SECONDARY SCHOOL | County | Boys |
| 03120101 | CHANGAMWE SECONDARY SCHOOL | County | Mixed |
| 03120102 | ST. CHARLES LWANGA SECONDARY SCHOOL | County | Mixed |
| 03120117 | MWIJABU SECONDARY SCHOOL | County | Mixed |
| 03120118 | CHAANI SECONDARY SCHOOL | County | Mixed |
| 03120121 | BOMU SECONDARY SCHOOL | County | Mixed |
| 03121204 | MWAKIRUNGE SECONDARY SCHOOL | County | Mixed |
| 03121216 | MTOPANGA MIXED SECONDARY SCHOOL | County | Mixed |
| 03121220 | HASSAN JOHO GIRLS’ SECONDARY SCHOOL | County | Girls |
| 03121226 | MARIMANI MIXED SECONDARY SCHOOL | County | Mixed |
| 03124105 | KAJEMBE HIGH SCHOOL | County | Mixed |
| 03124108 | MIRITINI SECONDARY SCHOOL | County | Mixed |
| 03124110 | JOMVU GIRLS HIGH SCHOOL | County | Girls |
| 03124111 | MIRITINI COMPLEX HIGH SCHOOL | County | Mixed |
| 03126106 | MAWENI MIXED SECONDARY SCHOOL | County | Mixed |
| 03126123 | FRERETOWN SECONDARY SCHOOL | County | Mixed |
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