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 Kilifi County:
| School Code & Name | Category | Type |
| 04102103 KATANA NGALA SECONDARY SCHOOL | Sub County | Mixed |
| 04102104 MAJAONI SECONDARY SCHOOL | Sub County | Mixed |
| 04102107 ROKA SECONDARY SCHOOL | Sub County | Mixed |
| 04102112 NGERENYA MIXED SECONDARY SCHOOL | Sub County | Girls |
| 04102115 UYOMBO GIRLS’ SECONDARY SCHOOL | Sub County | Mixed |
| 04102117 MDZONGOLONI HIGH SCHOOL | Sub County | Mixed |
| 04102119 MARAFIKI SECONDARY SCHOOL | Sub County | Mixed |
| 04102120 FUMBINI SECONDARY SCHOOL | Sub County | Mixed |
| 04107103 JILORE HIGH SCHOOL | Sub County | Mixed |
| 04107104 BARANI SECONDARY SCHOOL | Sub County | Mixed |
| 04107116 ACK CANON MWERI MEMORIAL SECONDARY SCHOOL | Sub County | Mixed |
| 04107120 F B TUVA MEMORIAL SECONDARY SCHOOL | Sub County | Mixed |
| 04107121 MEKATILILI MEMORIAL | Sub County | Mixed |
| 04107122 KIBOKONI SECONDARY SCHOOL | ||
| 04107124 LANGOBAYA SECONDARY SCHOOL | Sub County | Mixed |
| 04107127 MENYHART SECONDARY SCHOOL | Sub County | Mixed |
| 04107128 MUYEYE SECONDARY SCHOOL | Sub County | Mixed |
| 04107129 MBARAKACHEMBE SECONDARY SCHOOL | Sub County | Mixed |
| 04107131 KIJIWETANGA SECONDARY SCHOOL | Sub County | Mixed |
| 04107132 GANDA SECONDARY SCHOOL | Sub County | Mixed |
| 04107134 MIDA SECONDARY SCHOOL | Sub County | Mixed |
| 04107142 CHAKAMA SECONDARY SCHOOL | Sub County | Mixed |
| 04107143 JIMBA GEDE SECONDARY SCHOOL | Sub County | Mixed |
| 04107145 MAJIVUNI SECONDARY SCHOOL | Sub County | Mixed |
| 04107148 SABAKI SECONDARY SCHOOL | Sub County | Mixed |
| 04107149 MKONDONI SECONDARY SCHOOL | Sub County | Mixed |
| 04107150 MONGOTINI SECONDARY SCHOOL | Sub County | Mixed |
| 04107151 MADUNGUNI SECONDARY SCHOOL | Sub County | Mixed |
| 04107152 MAZIWANI SECONDARY SCHOOL | Sub County | Mixed |
| 04107153 ACK BISHOP KALU MIXED DAY SECONDARY SCHOOL | Sub County | Mixed |
| 04107154 BISHOP BALDACCHINO SECONDARY SCHOOL | Sub County | Mixed |
| 04107155 SOSOBORA SECONDARY SCHOOL | Sub County | Mixed |
| 04111011 MIYANI SECONDARY SCHOOL | Sub County | Mixed |
| 04111019 KINANI SECONDARY SCHOOL | Sub County | Mixed |
| 04111104 MAANDANI SECONDARY SCHOOL | Sub County | Mixed |
| 04111106 KIZURINI SECONDARY SCHOOL | Sub County | Mixed |
| 04111112 TSANGATSINI MIXED DAY SECONDARY SCHOOL | Sub County | Mixed |
| 04111113 KINARANI SECONDARY SCHOOL | Sub County | Mixed |
| 04111116 TSAGWA SECONDARY SCHOOL | Sub County | Mixed |
| 04111117 MWARENI SECONDARY SCHOOL | Sub County | Mixed |
| 04111118 MWIJO SECONDARY SCHOOL | Sub County | Mixed |
| 04111119 MUTSENGO SECONDARY SCHOOL | ||
| 04111120 MIGUNDINI SECONDARY SCHOOL | Sub County | Mixed |
| 04111121 MNAZIM’MWENGA SECONDARY SCHOOL | Sub County | Mixed |
| 04111122 MAKOMBOANI SECONDARY SCHOOL | Sub County | Girls |
| 04111124 KIRUMBI GIRLS SECONDARY SCHOOL | Sub County | Mixed |
| 04111125 SHANGIA SECONDARY SCHOOL | Sub County | Mixed |
| 04116107 PETANGUO SECONDARY SCHOOL | Sub County | Mixed |
| 04116108 DUNGICHA SECONDARY SCHOOL | Sub County | Mixed |
| 04116202 MITANGANI SECONDARY SCHOOL | Sub County | Mixed |
| 04116203 JILA SECONDARY SCHOOL | Sub County | Mixed |
| 04116204 BANDARI SECONDARY SCHOOL | Sub County | Mixed |
| 04116205 MIDOINA SECONDARY SCHOOL | Sub County | Mixed |
| 04116206 SHAKA SECONDARY SCHOOL | Sub County | Mixed |
| 04116304 BALE SECONDARY SCHOOL | Sub County | Mixed |
| 04116305 KACHORORONI SECONDARY SCHOOL | Sub County | Mixed |
| 04116306 SHANGWENI SECONDARY SCHOOL | Sub County | Mixed |
| 04116307 MAGOGONI SECONDARY SCHOOL | Sub County | Mixed |
| 04116308 AMASON JEFFAH KINGI SECONDARY SCHOOL | Sub County | Mixed |
| 04116309 NDUGUMNANI SECONDARY SCHOOL | Sub County | Mixed |
| 04119106 MARERENI SECONDARY SCHOOL | Sub County | Mixed |
| 04119107 MAJENJENI SECONDARY SCHOOL | Sub County | Mixed |
| 04119108 NGOMENI SECONDARY SCHOOL | Sub County | Mixed |
| 04119109 FUNDI – ISSA SECONDARY SCHOOL | Sub County | Mixed |
| 04119110 MAGARINI HILL SECONDARY SCHOOL | Sub County | Mixed |
| 04119112 KAEMBENI SECONDARY SCHOOL | Sub County | Mixed |
| 04119113 MJANAHERI SECONDARY SCHOOL | Sub County | Boys |
| 04119116 MAPIMO BOYS SECONDARY SCHOOL | Sub County | Mixed |
| 04119121 KURAWA SECONDARY SCHOOL | Sub County | Mixed |
| 04119202 MAGARINI SECONDARY SCHOOL | ||
| 04119203 ADU SECONDARY SCHOOL | Sub County | Mixed |
| 04119204 SHUJAA MEKATILILI SECONDARY SCHOOL | Sub County | Mixed |
| 04119205 GARASHI SECONDARY SCHOOL | Sub County | Mixed |
| 04119206 RAMADA MIXED SECONDARY SCHOOL | Sub County | Mixed |
| 04119207 SHOMELA SECONDARY SCHOOL | Sub County | Mixed |
| 04119209 WARESA SECONDARY SCHOOL | Sub County | Mixed |
| 04119211 DAGAMRA SECONDARY SCHOOL | Sub County | Mixed |
| 04122104 KASIDI SECONDARY SCHOOL | Sub County | Mixed |
| 04122106 KAMBE SECONDARY SCHOOL | Sub County | Mixed |
| 04122107 RABAI SECONDARY SCHOOL | Sub County | Mixed |
| 04122108 CHANG’OMBE SECONDARY SCHOOL | Sub County | Mixed |
| 04122109 BOFU SECONDARY SCHOOL | Sub County | Mixed |
| 04122110 KAJIWE SECONDARY SCHOOL | Sub County | Mixed |
| 04122111 MIKAHANI SECONDARY SCHOOL | Sub County | Mixed |
| 04122112 JIMBA SECONDARY SCHOOL | Sub County | Mixed |
| 04122113 REV CANON KURI MEMORIAL SECONDARY SCHOOL | Sub County | Mixed |
| 04122114 MBARARANI SECONDARY SCHOOL | Sub County | Mixed |
| 04122115 MWANDODO SECONDARY SCHOOL | Sub County | Mixed |
| 04122116 MIKOMANI SECONDARY SCHOOL | Sub County | Mixed |
| 04122117 BWAGAMOYO SECONDARY SCHOOL | Sub County | Girls |
| 04122118 KAWALA GIRLS SECONDARY SCHOOL | Sub County | Mixed |
| 04122119 CHIFERI SECONDARY SCHOOL | Sub County | Mixed |
| 04125101 MUSUMARINI SECONDARY SCHOOL | Sub County | Mixed |
| 04125102 TAKAUNGU SECONDARY SCHOOL | Sub County | Mixed |
| 04125103 SHARIANI SECONDARY SCHOOL | Sub County | Mixed |
| 04125107 K.P. SENIOR SECONDARY SCHOOL | Sub County | Mixed |
| 04125109 JUNJU SECONDARY SCHOOL | Sub County | Mixed |
| 04125110 MNARANI SECONDARY SCHOOL | ||
| 04125112 MAJAJANI SECONDARY SCHOOL | Sub County | Mixed |
| 04125116 ST JOSEPH HOUSE OF HOPE SECONDARY SCHOOL | Sub County | Mixed |
| 04125117 GONGONI SECONDARY SCHOOL | Sub County | Girls |
| 04125121 CITADEL MAIDEN SECONDARY SCHOOL | Sub County | Mixed |
| 04125125 MTEPENI SECONDARY SCHOOL | Sub County | Mixed |
| 04125126 MTOMONDONI SECONDARY SCHOOL | Sub County | Mixed |
| 04125214 VIPINGO SECONDARY SCHOOL | Sub County | Mixed |
| 04128101 JARIBUNI SECONDARY SCHOOL | Sub County | Mixed |
| 04128102 PALAKUMI SECONDARY SCHOOL | Sub County | Mixed |
| 04128103 MAYOWE SECONDARY SCHOOL | Sub County | Mixed |
| 04128104 VYAMBANI SECONDARY SCHOOL | Sub County | Mixed |
| 04128105 SOSONI SECONDARY SCHOOL | Sub County | Mixed |
| 04129202 ST. TERESA’S SECONDARY SCHOOL | Sub County | Mixed |
| 04129203 DZITSONI SECONDARY SCHOOL | Sub County | Mixed |
| 04129204 PAUL HARRIS HIGH SCHOOL | Sub County | Mixed |
| 04129205 CHASIMBA MIXED SECONDARY SCHOOL | Sub County | Mixed |
| 04129206 DINDIRI SECONDARY SCHOOL | Sub County | Mixed |
| 04129207 BUNDACHO SECONDARY SCHOOL | Sub County | Mixed |
| 04129208 MWARAKAYA SECONDARY SCHOOL | Sub County | Mixed |
| 04129209 KATIKIRIENI SECONDARY SCHOOL | Sub County | Mixed |
| 04129210 MBUYUNI SECONDARY SCHOOL | Sub County | Mixed |
| 04129211 BUNGU SECONDARY SCHOOL | Sub County | Girls |
| 04129212 NG’OMBENI GIRLS SECONDARY SCHOOL | Sub County | Mixed |
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