The American five-piece topped the poll above the likes of 5ive's 'Keep On Moving' and Westlife's 'Flying Without Wings'.
More than 7,000 music fans were surveyed by Amazepop to find the Top 50 boyband songs to enter the charts since 1998.
Teen heartthrobs One Direction made the most recent impact, storming up to second place with single 'What Makes You Beautiful', with two other singles, 'Live While We're Young' and 'Kiss You' also making the Top 50.
Other bands which feature in the list include Blue, Take That, 'N Sync and JLS, who recently announced that they are spitting after five years together.
The Top 10 voted boyband singles of the past 15 years are as follows:
1. Backstreet Boys - 'I Want It That Way'
2. One Direction - 'What Makes You Beautiful'
3. 'N Sync - 'Bye Bye Bye'
4. Westlife - 'Flying Without Wings'
5. 5ive - 'Keep On Moving'
6. McFly - 'All About You'
7. JLS - 'Everybody In Love'
8. Blue - 'All Rise'
9. Take That - 'Rule The World'
10. Jedward - 'Lipstick'ook
A similar poll by Amazepop saw Spice Girls hit 'Stop' crowned best girlband single of the past 15 years.
Watch the video for Backstreet Boys' 'I Want It That Way' below: