"Today at 2:20 p.m., our nation suffered a tragic air accident ... I am deeply saddened to announce the passing on of General Francis Omondi Ogolla," Ruto told reporters, adding that 11 others were on board and only two survived.
The helicopter came down in Elgeyo-Marakwet county, the president said.
Ruto said the air force has dispatched an air investigation team to establish the cause of the crash, which was about 400 kilometers northwest of the capital Nairobi.
Ogolla was previously the head of the Kenyan air force, before rising to deputy military chief and then being promoted by Ruto last year to head the military.
At least 10 soldiers were killed in June 2021 when their helicopter crashed while landing near the capital Nairobi.
Information for this report came from Reuters and AFP.