The suspects were accused of setting a dormitory on fire which killed two learners in 2010.
While delivering the judgement on Friday, Justice Jairus Ngaah said the prosecution did not prove its case beyond reasonable doubt.
Justice Ngaah cited that the investigating officer relied on circumstantial evidence to charge the accused.
The High Court in Nyeri has acquitted 11 former students of Endarasha Boys' Secondary and two locals accused of setting a school dormitory on fire which killed two learners in 2010.
While delivering the judgment Friday, Justice Jairus Ngaah ruled that the prosecution did not prove its case beyond reasonable doubt.