The guide said the isles had seven large puffin colonies, with the island of Foula offering the "most scenic" views of the seabirds.
But time could be running out to see the Atlantic puffins.
They are among four UK bird species now at risk of extinction, according to a global conservation database.
Atlantic puffins, European turtle doves, Slavonian grebes and pochards are on the International Union for Conservation of Nature's updated Red List of Threatened Species for birds.
Shetland is the only UK entry on the National Geographic list.
The others include Hawaii for seeing humpback whales and Madagascar for watching lemurs.
Shetland is the best destination for watching puffins according to a National Geographic list of the top 10 places to see wildlife.