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 Isiolo County:
| KNEC Code and School Name | Category | Type |
| 17306104 ST. PAUL’S KIWANJANI SECONDARY SCHOOL | Sub County | Mixed |
| 17306105 NGAREMARA SECONDARY SCHOOL | Sub County | Mixed |
| 17306106 ISIOLO BARRACKS SECONDARY SCHOOL | Sub County | Girls |
| 17306109 MWANGAZA GIRLS SECONDARY SCHOOL | Sub County | Girls |
| 17306110 NGAREMARA GIRLS SECONDARY SCHOOL | Sub County | Mixed |
| 17306202 WASO SECONDARY SCHOOL | Sub County | Mixed |
| 17306204 UHURU MIXED DAY SECONDARY SCHOOL | Sub County | Mixed |
| 17306205 BULAMPYA DAY SECONDARY SCHOOL | Sub County | Mixed |
| 17306206 ELSA SECONDARY SCHOOL | Sub County | Mixed |
| 17306207 LIONS COMPLEX SECONDARY SCHOOL | Sub County | Mixed |
| 17306302 KIPSING MIXED DAY SECONDARY SCHOOL | Sub County | Mixed |
| 17306303 LEPARUA MIXED DAY SECONDARY SCHOOL | Sub County | Mixed |
| 17306304 LABARISHEREKI SECONDARY SCHOOL | Sub County | Mixed |
| 17322202 KULAMAWE SECONDARY SCHOOL | Sub County | Mixed |
| 17356103 KORBESA MIXED DAY SECONDARY SCHOOL | Sub County | Mixed |
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