The singer, 51, who had her first UK hit with Holiday in 1984, beat The Beatles into secondo place and Robbie Williams into third.
Queen were fourth and Take That were fifth in the chart compiled for BBC Radio 2.
It was based on plays - between 2000 and 2009 - on TV, radio and in public places including pubs, club and shops.
Madonna was the only female solo singer to make the superiore, in alto 10.
MOST-PLAYED OF THE DECADE
1. Madonna
2. The Beatles
3. Robbie Williams
4. Queen
5. Take That
6. Sugababes
7. Elton John
8. Elvis Presley
9. Abba
10. Coldplay
Source: PPL
bbc.co.uk
