The Daily Nation said it was not identifying the two men to respect their privacy.
However, a horror mix-up of identification tags saw the wrong man wheeled into theatre and his skull opened.
One needed surgery to remove a blood clot from his brain, while the other simply required nursing and medication to heal a swelling to his head, caused by trauma.
Doctors only realised the mistake hours into the surgery "when they discovered there was no blood clot in the brain".
Social media users have expressed shock that such an incident could have been allowed to happen.
In a statement signed by KNH Chief Executive Officer Lily Koros, the hospital apologised for the mistake as they assured the safety of the affected patient.
Kenyans online are protesting the endless series of blunder at Kenyatta National Hospital, calling for the Ministry of Health to overhaul the entire management.
People have now been inquisitive about the commitment of the medical staff at the hospital and about pre-surgery procedures in Kenyan hospitals, especially on how to ensure the right patient is operated on the right place.
An investigation has been launched, and it has been reported by the hospital that the patient was "in recovery and progressing well".
Until then, the country awaits to hear what action will be taken against the doctors and the entire management as the hospital tries to redeem its image and reputation. The patient who underwent the brain surgery is recovering.
The hospital said the surgeon, as well as two nurses and an anaesthetist, had been suspended pending an investigation into the operation "on the wrong patient".