Dubbed the "killer cop" by media outlets, Ahmed Rashid was filmed shooting the two young men as they lay on the ground on a busy street in the capital Nairobi on March 31, 2017.
The Independent Policing Oversight Authority (IPOA) watchdog recommended murder charges against him last November, saying that its investigation into the deaths "established that the fatalities were occasioned by police action."
But Rashid contested the charges, telling the Nairobi high court that he was a law-abiding police officer who was carrying out his duty.
He was arrested and immediately released on bail of 200,000 Kenyan shillings ($1,500) on Monday, following an application by his lawyers.
Kenyan police are often accused by rights groups of using excessive force and carrying out unlawful killings, especially in poor neighbourhoods.
Last October, President William Ruto disbanded a feared 20-year-old police unit accused of extrajudicial killings and vowed an overhaul of the security sector.
Kenya's parliament established the IPOA in 2011 to provide civilian scrutiny of a powerful institution also reputed to be among the country's most corrupt.
Only around a dozen officers have been convicted as a result of IPOA investigations, even though the watchdog has examined more than 6,000 cases of alleged police misconduct, according to data covering the period from its inception to July 2021.
Activists largely defend the IPOA's record, saying police often frustrate inquiries by refusing to cooperate.
Kenya Cop Pleas 'Not Guilty' For Killings
FILE: Illustration of a pair of handcuffs hanging on dark background. Taken March 3, 2019.
NAIROBI - A Kenyan police officer accused of murdering two teenagers in 2017 pleaded not guilty to the charges on Monday, in a case that raised questions about extrajudicial killings after video footage of the shootings went viral.