The 54-year-old singer has topped the annual rundown of the top money-makers for the second time in five years.
Her 88-date MDNA world tour, 2012's most successful, helped her take home $34.6m (£26.1m), Billboard said.
Concerts account for 68.9% of the total revenues for the 40 artists on the list, which estimates annual earnings.
According to the figures, compiled using Boxscore concert data and Nielsen SoundScan sales information, Bruce Springsteen came a close second.
He earned $33.4m (£25.3m) after touring to sold-out stadiums and arenas on the back of his number one album Wrecking Ball.
Strong merchandise sales helped with his earnings, with Springsteen's live shows making up 92% of his overall revenue.
Waters came third with earnings from his large scale The Wall Live tour estimated at $21m (£16m).
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MUSIC'S TOP EARNERS IN 2013
1 Madonna - $34.6m
2 Bruce Springsteen - $33.4m
3 Roger Waters - $21m
4 Van Halen - $20m
5 Kenny Chesney - $19.1m
6 Dave Matthews Band - $18.9m
7 Tim McGraw - $18.3m
8 Jason Aldean - $17.6m
9 Coldplay - $17.3m
10 Justin Bieber - $15.9m
Source: Billboard
Van Halen were in fourth position with $20m (£15.3m) after touring in support of their album A Different Kind of Truth.
Speaking about the list, Billboard editorial analyst Glenn Peoples said the most money "always comes from high-paying live performances".
He said: "Ironically, the most popular touring artists are usually well past their peaks on the album sales charts."
The rest of the top 10 included country music veteran Kenny Chesney in fifth, followed by the Dave Matthews Band, country's Tim McGraw and Jason Aldean, and British band Coldplay.
Canadian teen star Justin Bieber completed the top 10, earning up to $16m (£12.1m), of which $10m (£7.6m) came from his sold-out Believe tour.
"The entire top 10 averaged 84.2% of their income from concerts, and the number would have been higher, if not for Justin Bieber's mere 60.1% share at number 10 dragging down the average," said Peoples.
Madonna is the only woman in the top 10 after last year's victor Taylor Swift fell to 15th place because she did not tour last year.
Swift still did well, earning $12.7m (£8.4m) from more than three million digital albums and 15.6 million digital songs.
Meanwhile, Adele, who had the biggest-selling album of the year in the US in 2011 and 2012, came in 11th place, earning $14m (£10.6m).
She did not tour last year but took the year out to have a baby while her second album 21 continued to sell well in physical and digital formats.
