Unlike the north polar region, which is preferred especially for flights between Asia and North America, it is not possible to come across passenger planes over Antarctica.
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The short answer is, no, it's not illegal to fly over Antarctica. But there are practical considerations that make it challenging for regular airlines to navigate across the land. In many parts of Antarctica, there's limited or no infrastructure, no landing strips, and obviously no refuelling stations for planes.
Thanks to the low visibility and undeveloped infrastructure, flying over Antarctica is extremely difficult. Specifically, because of the strong magnetic fields that surround the polar regions, navigating there, no matter how well-equipped the airplane is in terms of instrumentation, can be particularly challenging.
For anyone planning to fly to/ from Antarctica, the town of Punta Arenas in southern Chile is the main departure point for all: Charter flights to King George Island, South Shetland Islands (flying time = 2 hours). This is the only commercial airfield servicing the Antarctic Peninsula for visitors.
There aren't actually any commercial airports in Antarctica, so to reach Antartica, you'll have to take a flight to Antartica's closest commercial airport in Punta Arenas, Chile, and then take a cruise or a fly & cruise from Punta Arenas to Antartica.
Phoenix Runway, which was completed in 2016 to replace an older facility, is made of snow so tightly packed that it can withstand the landings of heavy-wheeled aircraft like the USAF Boeing C-17 Globemaster III. Williams Field, another snowy runway near McMurdo, offers a place for ski-equipped aircraft to land.
The most common reason is that there are no airstrips or airports on many of the small islands, so if a plane had to make an emergency landing, it would be difficult to find a place to land. Additionally, the Pacific Ocean is vast and remote, so if a plane were to go down, it would be very difficult to find.
Travelers do not need permission to go to Antarctica, but tourism operators must hold a valid permit. First, a bit of background on why it is legal to visit Antarctica. Antarctica is not a country. The continent is protected by the Antarctic Treaty, which preserves it for peaceful and scientific use.
There is also a risk of mistaken identity in or near the ZKKP/Pyongyang FIR boundary, as North Korea are threatening to actively shoot down reconnaissance aircraft in their airspace. The US prohibits flights across all North Korean airspace, including the oceanic part of the ZKKP/Pyongyang FIR over the Sea of Japan.
You might think circling the globe by airplane is no big deal anymore. But you'd be wrong. Surprisingly, circumnavigating the world via the North Pole to the South Pole in an airliner is a feat accomplished only three times.