Sub County Schools in Kenya form the lowest cadre of secondary schools; after National, Extra County schools and County Schools, respectively. The schools admit students from majorly within the Sub country; from the immediate locality. The Schools are majorly of Mixed type; though there are a few single sex schools. Students joining these schools are mostly those with the low marks in the Kenya Certificate of Primary Education, KCPE, exams. The schools are in most cases Day Schools; though some are Day and Boarding Schools. These schools form the majority of secondary schools in Kenya and are found in all Counties.
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Here are the Sub County Schools in Lamu County:
| School Code & Name | Category | Type |
| 06104204 HONGWE SECONDARY SCHOOL | Sub County | Mixed |
| 06104205 BAHARI SECONDARY SCHOOL | Sub County | Mixed |
| 06104206 UZIWA SECONDARY SCHOOL | Sub County | Mixed |
| 06104208 LAKE KENYATTA SECONDARY SCHOOL | Sub County | Mixed |
| 06104209 MAJEMBENI SECONDARY SCHOOL | Sub County | Mixed |
| 06104210 KIONGWE MIXED DAY SECONDARY SCHOOL | Sub County | Mixed |
| 06104212 BOMANI SECONDARY SCHOOL | Sub County | Mixed |
| 06104302 WITU MJINI SECONDARY SCHOOL | Sub County | Mixed |
| 06118102 KIZINGITINI SECONDARY SCHOOL | Sub County | Mixed |
| 06118103 SIYU SECONDARY SCHOOL | Sub County | Mixed |
| 06118201 KIUNGA SECONDARY SCHOOL | Sub County | Mixed |
| 06130102 MATONDONI SECONDARY SCHOOL | Sub County | Girls |
| 06130103 BRIGHT GIRLS SHELLA SECONDARY SCHOOL | Sub County | Mixed |
| 06130104 WIYONI SECONDARY SCHOOL | Sub County | Mixed |
| 06130201 MOKOWE SECONDARY SCHOOL | Sub County | Mixed |
| 06130202 HINDI SECONDARY SCHOOL | Sub County | Mixed |
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