The fire, which occurred on Thursday night, has left several other students with severe burns, with more than a dozen hospitalised.
There are fears the death toll could rise as authorities continue to investigate.
The cause of the fire remains unknown, and police are working to determine what triggered the deadly blaze.
President William Ruto described the incident as "horrific" and "devastating" in a social media post, assuring the public that "those responsible will be held to account." He has ordered a thorough investigation into the tragedy.
The fire broke out around midnight when more than 150 pupils were inside the dormitory.
The blaze spread quickly, particularly because many of the school's buildings are made of timber, according to local reports.
Police spokesperson Resila Onyango noted that many of the bodies recovered were "burnt beyond recognition," and additional bodies might be found as the scene is further processed.
President William Ruto President William Ruto Pulse Live Kenya Emergency response teams, including the Kenya Red Cross, are providing trauma counselling to the affected pupils, teachers, and families.
The organisation has also set up a tracing desk at the school to assist families in locating their loved ones.
Hillside Endarasha Academy, a private primary school located near Nyeri town, has over 800 students, mostly aged between five and 12 years.
This tragedy recalls similar past incidents in Kenyan boarding schools.
In 2017, a fire at Moi Girls High School in Nairobi claimed the lives of 10 students in an arson attack, while the deadliest school fire in Kenya occurred over 20 years ago in Machakos County, killing at least 67 students.