Eoin Colfer's work was voted the ultimate "Puffin of Puffins" in a readers' poll.
The author described receiving the accolade as "my proudest professional moment".
More than 10,000 votes were cast online. Colfer's best-selling story of child prodigy Artemis Fowl came out on top with a huge 68 per cent of the vote. Worldwide sales of the title have now reached about 20 million.
Roald Dahl's Charlie and the Chocolate Factory was in second place with 13 per cent.
Colfer said: "I am beyond thrilled by this result. To be chosen by Puffin as a modern classic is a huge honour."