A time tunnel is used to travel through time. These tunnels are mentioned in The Lost Colony and The Time Paradox and is used, on many occasions, by N°1 to bring Artemis Fowl and Holly Short back to Earth or their own time.
Both Holly and Artemis have been through a time tunnel four times. The second time they went through they switched an eye each. When they went through the first time Artemis obtained some fairy magic.