Kilifi County has about 18 county secondary schools. 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 Kilifi County in no particular order.
Some of these schools are the best performing county schools in the Kilifi region.
Here is a list of all the County schools in Kilifi County:
| School Code | School Name | Category | Type | County |
| 04102101 | KILIFI TOWNSHIP SECONDARY SCHOOL | County | Boys | Kilifi |
| 04102102 | CHUMANI SECONDARY SCHOOL | County | Mixed | Kilifi |
| 4102114 | ST. THOMAS GIRLS’ SECONDARY SCHOOL | County | Girls | Kilifi |
| 04107102 | GEDE SECONDARY SCHOOL | County | Boys | Kilifi |
| 04107108 | KAKUYUNI BOYS SECONDARY SCHOOL | County | Boys | Kilifi |
| 04111103 | MARIAKANI SECONDARY SCHOOL | County | Boys | Kilifi |
| 04111105 | CHANAGANDE SECONDARY SCHOOL | County | Mixed | Kilifi |
| 04111107 | NGALA MEMORIAL SECONDARY SCHOOL | County | Mixed | Kilifi |
| 04111108 | MOI KADZONZO GIRLS SECONDARY SCHOOL | County | Girls | Kilifi |
| 04111123 | KALOLENI GIRLS SECONDARY SCHOOL | County | Girls | Kilifi |
| 4116101 | GANZE BOYS SECONDARY SCHOOL | County | Boys | Kilifi |
| 4116103 | GANZE GIRLS SECONDARY SCHOOL | County | Girls | Kilifi |
| 4116301 | VITENGENI BAPTIST SECONDARY SCHOOL | County | Mixed | Kilifi |
| 4116303 | MWANGEA GIRLS’ SECONDARY SCHOOL | County | Girls | Kilifi |
| 4119101 | GALANA SECONDARY SCHOOL | County | Mixed | Kilifi |
| 4119105 | MAPIMO GIRLS SECONDARY SCHOOL | County | Girls | Kilifi |
| 4119201 | MARAFA SECONDARY SCHOOL | County | Mixed | Kilifi |
| 04129201 | LUTSANGANI BOYS SECONDARY SCHOOL | County | Boys | Kilifi |
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, which is education.go.ke.