That also means it was the airport's busiest month ever measured by number of passengers.
"The high season no longer ends when the summer holidays end," the airport's chief commercial officer Peter Krogsgaard said. "In September we had almost as many travellers as we do in the summer months."
He added that this is particularly due to the fact that Copenhagen is a popular transit airport.
"At the same time, many Danes and southern Swedes choose to either extend their summer with hot weather and sunshine down south, head out on a big city holiday in Europe or a trip over the Atlantic to the US."
Copenhagen Airport is the largest airport in Scandinavia, serving much of Denmark and southern Sweden.
The most popular destination was Norway, with 270,000 passengers flying there from Copenhagen last month. Next up was Spain, with 255,000 passengers, and the UK, with 245,000 passengers.
The most popular destination cities were London, Stockholm, Oslo, Amsterdam and Paris.
The airport also said that there is growing interest in routes between Copenhagen and the US, with an eight percent increase on September last year. This year, 140,000 people flew on direct routes between Copenhagen and the US.
"We see a clear increase in traffic between Denmark and the US," Krogsgaard said. "There's growth on the direct routes and at the same time there are more American guests coming to Denmark."
Copenhagen Airport is the only Danish airport with direct routes to the US, with SAS, Delta and American Airlines running a total of 12 routes from Copenhagen to US cities.
The most popular US city was New York, followed by San Francisco, Boston and Chicago.
"Denmark is a popular destination for the Americans and direct flights make it easy to get here. Some people have Denmark and Copenhagen as their final destination, but others head further out into Europe," he said.
It expects a total of 1.1 million passengers to pass through the airport in October, in part due to the autumn school holiday this month.
Spain, Italy and France are the most popular destinations in southern Europe, with an estimated 220,000 people flying from Copenhagen around week 42, October 12th to 18th. Sweden's autumn holiday is two weeks later in week 44 (October 26th-30th).