The annual survey, conducted by France Football magazine, estimates Messi’s earnings at £29.6 million, £2.3m ahead of Beckham.
The Englishman – who is currently out with a long-term injury – remains in second place on the list, just £100,000 ahead of Real Madrid winger Cristiano Ronaldo.
Messi’s salary is made up of a £9m basic wage, £3.6m in bonuses and a further £17.1m in personal endorsements. The Argentine has deals with companies including Adidas, Pepsi and Gillette.
The top English-based played is Manchester City striker Carlos Tevez, who comes in seventh with £13.8m, while Chelsea’s Frank Lampard is ninth on £12.7m
Internazionale boss Jose Mourinho is the best paid manager in the game with £11.7m, just ahead of Manchester City boss Roberto Mancini on £10.8m.
Top-earning players in football:
1. Lionel Messi (Barcelona) £29.6m
2. David Beckham (LA Galaxy) £27.3m
3. Cristiano Ronaldo (Real Madrid) £26.9m
4. Kaka (Real Madrid) £16.9m
5. Thierry Henry (Barcelona) £16.2m
6. Ronaldinho (AC Milan) £15.4m
7. Carlos Tevez (Manchester City) £13.8m
8. Zlatan Ibrahimovic (Barcelona) £13m
9. Frank Lampard (Chelsea) £12.7m
10. Samuel Eto’o (Inter Milan) £12.4m