Ed Chen Junyuan, 37, and Tay Miow Seng, 40, were each charged with operating unauthorized operation of a small unmanned aircraft within 5 kilometres of Paya Lebar Air base.
The men face a maximum fine of SGD 20,000 (US$14,700) if found guilty. They will return to court on Aug 2.
The men are the first individuals to be charged with this particular offence following the drone activity that disrupted operations at Changi Airport in June.
According to the Civil Aviation Authority of Singapore, no one is allowed to fly drones within 5 kilometres of airports and military airbases, or at altitudes above 60 metres without a permit in the country.
Popular use of drones has pose great challenge for air traffic in many countries. Last year, Gatwich Airport in London had to cease operation due to the presence of unmanned aerial vehicle, affecting tens of thousands of passengers.