The rankings is based on overall earnings which includes salaries, winnings from respective sports and endorsement deals all amassed over the period between June 2018 to June 2019.
Last year's highest earner, boxer Floyd Mayweather, dropped off the list completely.
Serena Williams is the only woman in the top 100, earning $29.2m (£22.9m).
Athletes from 10 sports made the top 100, with National Basketball Association stars leading the way.
And Messi was named the highest paid athlete for the first time, moving one position from previous year thanks to a staggering earnings of $127m (R1.87bn).
"The global impact of soccer is clearly reflected in earnings in 2019, with the top three athletes on the list being Messi, Ronaldo, and Neymar", Badenhausen said on the official website.
The stars of Barça, Juventus and PSG are the only footballers in the top 10 of the list, which is made up of: Canelo Alvarez (boxing), Roger Federer (tennis), Russell Wilson (American football), Aaron Rodgers (American football), LeBron James (basketball), Stephen Curry (basketball) and Kevin Durant (basketball).
Messi, who scored 36 goals while leading Barcelona to the La Liga title this year, earned $127 million (£100 million) between his salary and endorsements to move up one spot on the list of the world's 100 highest-paid athletes.
Los Angeles Lakers star LeBron James was the highest earning National Basketball Association player, with $89 million, while Golden State's Stephen Curry was ninth with $79.8 million.