The France captain scored 10 goals to top the charts ahead of Argentina great Messi, who finished with eight.
England midfielder Jude Bellingham and Norway striker Erling Haaland each scored seven times.
Real Madrid forward Mbappe, 27, also won the prize with eight goals at the 2022 World Cup in Qatar, where France were beaten finalists.
The Frenchman, who made his World Cup debut in 2018, scored twice in Saturday’s third-place play-off, which England won 6-4.
Mbappe is now the top scorer in World Cup history, with 22 goals across three World Cups, one ahead of Messi, who failed to sparkle in Sunday’s 1-0 defeat by Spain.
“When you score that many goals in the World Cup, it certainly takes you to a whole new level,” he said after the match against England.
“But I would have preferred not to be the top scorer and to have played in the final. It’s good for my legacy once I’ve retired, but right now, that’s not what’s on my mind.”
Outgoing France coach Didier Deschamps, who has guided Mbappe through each of his World Cup campaigns, said: “He’s an extraordinary player. He is a brilliant captain.”
Spain midfielder Rodri won the Golden Ball award for player of the tournament, while his teammate Unai Simon claimed the Golden Glove award for best goalkeeper after conceding just once in eight games.
Spain defender Pau Cubarsi, 19, won the Fifa young player award. (AFP)
