Tokyo, which held the top spot last year, was pushed to the fourth position after Thailand's Bangkok and Singapore.
Kyoto is Japan's cultural capital, renowned for its 14 UNESCO world heritage sites, centuries-old Buddhist temples and Shinto shrines.
The annual best Asian city awards recognize the region's leading destinations, hotels and travel experiences based on factors such as visitor satisfaction, hospitality standards, service quality and overall tourism offerings.
10 best cities in Asia-Pacific:
1. Kyoto
2. Bangkok
3. Singapore
4. Tokyo
5. Hong Kong
6. Sydney
7. Ho Chi Minh City
8. Seoul
9. Kuala Lumpur
10. Chiang Mai