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Hong Kong has a highly developed transport network. There is no problem getting to the city from the airport, even after midnight. You can choose go by Airport Express, buses, and a taxi.
Airport Express is probably the fastest way. There are only three stops at Tsing Yi, Kowloon and Hong Kong Stations, getting you to the city in less than 25 minutes.
If you are staying on Hong Kong Island like Central, Causeway Bay, and Wan Chai, it is good choice.
But if you are going to Kowloon, such as Tsim Sha Tsui, Jordan, Mong Kok, you need to get a shuttle bus from Kowloon Station. Kowloon Station is actually not close to the hub of the city.
On the way back to the airport, there is a good deal for Airport Express passengers : the check in of the flight could be done in Hong Kong and Kowloon Stations. That means your luggages will be directly sent to the airport. You only need to arrive the boarding gate 30 minutes earlier.
Opening hours :
From the airport 5:54am to 00:48am
From Hong Kong Station 5:50am to 00:48am
Comparing to Airpress Express, airport buses cost cheaper, less than HKD$40 for a single journal. Cash and octopus card payment is acceptable, but no cash change on the bus.
Basically it takes 40 minutes to the city and drop you off to most of the hotel.
With providing 24 hours service, there are still lots of bus routes going to both of Kowloon and Hong Kong Island after mid-night.
If money is not one of your concern, and you are so tired after a long flight, taking a taxi would be a good option.
It takes 40-60 minutes to the main destinations on Kowloon and Hong Kong Island from HKD$250 to $300. Some of the taxi drivers might overcharge the passengers, so be careful of it.