The 36-year-old welterweight - considered the best defensive boxer of his generation - topped the magazine's Fortunate 50 list, issued on Wednesday. Mayweather also took the top spot last year, earning an estimated $85 million, again from just two fights, the magazine reported.
Miami Heat basketball star LeBron James, 28, a four-time NBA Most Valuable Player, came in this year in the number two slot, earning a total of $56.5 million.
The list is calculated by combining estimated salary, winnings and endorsements. Mayweather's total earnings are even more impressive considering he received no endorsement money either this year or last.
James' $56.5 million income combines a $17.5 million salary with an additional $39 million in endorsements.
Golfer Tiger Woods, the highest paid US athlete from 2004, when the list was first published, through 2011, dropped to the No. 5 slot on this year's list, earning $40.8 million.
Chicago Cubs outfielder Alfonso Soriano came in as the 50th highest-paid US athlete with an estimated $18.2 million.
Candidates for the list must be US citizens and compete in a US-based league.
Internationally, David Beckham is estimated to earn more than $48 million, landing him the top spot on the magazine's annual list of highest-paid athletes worldwide, The International 20.
Top 10 (total/salary/endorsements)
1. Floyd Mayweather Jr. Boxing $90,000,000 / $90,000,000 / $0
2. LeBron James NBA $56,545,000 / $17,545,000 / $39,000,000
3. Drew Brees NFL $47,800,000 / $40,000,000 / $7,800,000
4. Kobe Bryant NBA $46,850,000 / $27,850,000 / $19,000,000
5. Tiger Woods Golf $40,839,027 / $7,839,027 / $33,000,000
6. Phil Mickelson Golf $39,528,630 / $3,528,630 / $36,000,000
7. Derrick Rose NBA $33,403,000 / $16,403,000 / $17,000,000
8. Peyton Manning NFL $31,000,000 / $18,000,000 / $13,000,000
9. Alex Rodriguez MLB $29,900,000 / $29,000,000 / $900,000
10. Zack Greinke MLB $29,020,000 / $29,000,000 / $20,000