What is a County School? County schools in Kenya fall below extra-county schools in the national school ranking. There are hundreds of extra county schools in Kenya. County school institutions are part of the four-tier secondary school system in the country. This article lists the county schools in Mombasa county in no particular order.
Some of these schools are the best performing county schools in the Mombasa region.
| School Code | School Name | Category | Type | County |
| 03106101 | ALLIDINA VISRAM HIGH SCHOOL | County | Boys | Mombasa |
| 03106103 | TUDOR DAY SECONDARY SCHOOL | County | Boys | Mombasa |
| 03106105 | STAR OF THE SEA HIGH SCHOOL | County | Girls | Mombasa |
| 03106107 | SACRED HEART HIGH SCHOOL, MOMBASA | County | Mixed | Mombasa |
| 03106116 | SERANI SECONDARY SCHOOL | County | Boys | Mombasa |
| 03106118 | SHARIFF NASSIR GIRLS | County | Girls | Mombasa |
| 03106121 | MBARAKI GIRLS SECONDARY SCHOOL | County | Girls | Mombasa |
| 03106122 | TONONOKA SECONDARY SCHOOL | County | Boys | Mombasa |
| 03106124 | ALFARSY GIRLS SECONDARY SCHOOL | County | Girls | Mombasa |
| 03106125 | MVITA BOYS SECONDARY SCHOOL | County | Boys | Mombasa |
| 03106132 | MAKANDE GIRLS SECONDARY SCHOOL | County | Girls | Mombasa |
| 03106133 | MAKUPA BOYS SECONDARY SCHOOL | County | Boys | Mombasa |
| 03108101 | MOI FORCES ACADEMY-MOMBASA | County | Mixed | Mombasa |
| 03108103 | MTONGWE GIRLS SECONDARY SCHOOL | County | Girls | Mombasa |
| 03108104 | SHIKAADABU SECONDARY SCHOOL | County | Mixed | Mombasa |
| 03108114 | MWAHIMA SECONDARY SCHOOL | County | Mixed | Mombasa |
| 03108201 | LIKONI SECONDARY SCHOOL | County | Boys | Mombasa |
| 03108209 | PUMA SECONDARY SCHOOL | County | Mixed | Mombasa |
| 03108211 | MRIMA MIXED DAY SECONDARY SCHOOL | County | Mixed | Mombasa |
| 03108217 | BUBUBU BOYS SECONDARY SCHOOL | County | Boys | Mombasa |
| 03120101 | CHANGAMWE SECONDARY SCHOOL | County | Mixed | Mombasa |
| 03120102 | ST. CHARLES LWANGA SECONDARY SCHOOL | County | Mixed | Mombasa |
| 03120117 | MWIJABU SECONDARY SCHOOL | County | Mixed | Mombasa |
| 03120118 | CHAANI SECONDARY SCHOOL | County | Mixed | Mombasa |
| 03120121 | BOMU SECONDARY SCHOOL | County | Mixed | Mombasa |
| 03121204 | MWAKIRUNGE SECONDARY SCHOOL | County | Mixed | Mombasa |
| 03121216 | MTOPANGA MIXED SECONDARY SCHOOL | County | Mixed | Mombasa |
| 03121220 | HASSAN JOHO GIRLS’ SECONDARY SCHOOL | County | Girls | Mombasa |
| 03121226 | MARIMANI MIXED SECONDARY SCHOOL | County | Mixed | Mombasa |
| 03124105 | KAJEMBE HIGH SCHOOL | County | Mixed | Mombasa |
| 03124108 | MIRITINI SECONDARY SCHOOL | County | Mixed | Mombasa |
| 03124110 | JOMVU GIRLS HIGH SCHOOL | County | Girls | Mombasa |
| 03124111 | MIRITINI COMPLEX HIGH SCHOOL | County | Mixed | Mombasa |
| 03126106 | MAWENI MIXED SECONDARY SCHOOL | County | Mixed | Mombasa |
| 03126123 | FRERETOWN SECONDARY SCHOOL | County | Mixed | Mombasa |
All the county schools in Kenya admit students majorly from within the County they are located in. Admission of form ones is done through the Education Ministry’s Portal and the admission letters to these schools are downloaded from the Ministry’s website.