Bad weather has killed 37 people in the Chinese capital in the past week while at least seven others are missing.
On 20 July, much of the city was shut down by a huge storm but the palace's official Sina Weibo said it was one of the few areas that remained open.
It even took in 30,000 visitors during the storm, it said.
China has battled serious floods throughout its history, and the designers of the Forbidden City would have been well aware of the need to build in proper defences.
The palace published a series of images on Weibo showing heavy flooding in the 600-year-old courtyards, but the drainage system in action removing the water.
State media quoted an unnamed official as saying the combination of cleverly designed sloping courtyards, stepped buildings and underground drains meant water could be carried away in 20 minutes.
The palace's original photos of the floods were later taken down - an official told BBC News that was because they did not know who had taken them.
But the original post and new images have been circulating on local news portals and social media.
The large volume of water in some of the pictures prompted some on popular Chinese micro-blogging site Weibo to question the "ancient engineering efforts".
"A royal drainage system? It still looks very flooded to me," commented one netizen.
"Engineering level: Ancient China," said another.
Other users questioned the loss of lives during the rainy season and called for "more serious action" with regards to the floods.
"Why couldn't this 600-year-old system have been used for other buildings as well if it's so effective? Many lives could have been saved," commented a Weibo user going by the name of Cisi Fang 52.
Officials from Beijing's Forbidden City have said an ancient drainage system protected it during recent heavy rains and intense flooding.