Sub county schools are the lowest cadre of secondary schools in Kenya. They are mostly made up of small mixed day schools, although there are well-established girls or boys only boarding sub-county schools across the country. The list below consists of names, KNEC Codes, Category and Types of sub county schools in Kisii County.
| KNEC CODE | School Code | Category |
| 40727119 | Kebabe S.D.A Secondary School | Sub County |
| 40732111 | Kiobegi Secondary School | Sub County |
| 40732112 | Nyabite A.C Secondary School | Sub County |
| 40732113 | St Charles Kabeo Secondary School | Sub County |
| 40732115 | St. James Gionsaria Secondary School | Sub County |
| 40732116 | Rogongo Deb Mixed Secondary School | Sub County |
| 40732117 | Nyabite Dok Secondary School | Sub County |
| 40732118 | Mosora Sda Secondary School | Sub County |
| 40732119 | St. John’s Orogare Secondary School | Sub County |
| 40732121 | St. Thomas Turwa Secondary School | Sub County |
| 40732123 | Itumbe Dok Secondary School | Sub County |
| 40732124 | Nyachogochogo Aic Secondary School | Sub County |
| 40732125 | Ebigogo Secondary School | Sub County |
| 40732126 | St. Gabriel Riyabo Secondary School | Sub County |
| 40732130 | Nyabisia Deb Mixed Secondary School | Sub County |
| 40732201 | Naikuru P.A.G Secondary School | Sub County |
| 40732202 | Isena P.A.G Secondary School | Sub County |
| 40732203 | St Paul’s Nyacheki Secondary School | Sub County |
| 40732204 | Mochengo P.A.G Secondary School | Sub County |
| 40732205 | Nyangusu Mixed Secondary School | Sub County |
| 40732208 | Borangi S.D.A Secondary | Sub County |
| 40732209 | Nyamakorobo F.A.M Secondary School | Sub County |
| 40732210 | Kionduso P.A.G. Secondary School | Sub County |
| 40732211 | Getai Sda Mixed Secondary School | Sub County |
| 40732212 | Mogonga P.A.G Secondary School | Sub County |
| 40732213 | The Sacred Heart Of Jesus Ekeonga Secondary School Sub County | Sub County |
| 40732214 | Ebiosi P.A.G Mixed Secondary School | Sub County |
| 40732216 | Nyamuya Elck Secondary School | Sub County |
| 46802012 | Makaror Mixed Day Secondary School | Sub County |
| 46802013 | Shaletey Mixed Day Secondary School | Sub County |
| 46802014 | Barwaqo Mixed Day Secondary School | Sub County |
| 46802104 | Furaha Mixed Day Secondary School | Sub County |
| 46802106 | Waberi Mixed Day Secondary School | Sub County |
| 46802108 | The Faulu Secondary School | Sub County |
| 46802109 | Ahmed Liban Secondary School | Sub County |
| 46807103 | Bute Mixed Day Secondary School | Sub County |
| 46808103 | Hadado Secondary School | Sub County |
| 46808104 | Ademasajida Mixed Day Secondary School | Sub County |
| 46808106 | Lagbogol Secondary School | Sub County |
| 46809101 | Leheley Secondary School | Sub County |
| 46809201 | Diif Secondary School | Sub County |
| 46813102 | Eldas Girls Secondary School | Sub County |
| 46813103 | Tula Tula Secondary School | Sub County |
| 46819102 | Buna Girls Secondary School | Sub County |
| 46820103 | Habaswein Mixed Day Secondary School | Sub County |
| 46820105 | Biyamathow Mixed Day And Boarding Secondary School Sub County | Sub County |
| 46820106 | Inshaallah High School | Sub County |
| 46820107 | Abakore Mixed Day Secondary School | Sub County |
| 46820108 | Sabuli Mixed Day&Boarding Secondary School | Sub County |
| 47803107 | Barwaqo Boys Day Secondary School | Sub County |
| 47803109 | Khadija Girls Day Secondary School | Sub County |
| 47803110 | Buruburu Day Boys Secondary School | Sub County |
| 47803115 | Kamor Secondary School | Sub County |
| 47803117 | Duse Boys Secondary School | Sub County |
| 47803120 | Elimu Bora Mixed Secondary School | Sub County |
| 47803121 | Mandera Dimtu Girls Secondary School | Sub County |
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