Let me start off by saying that iTunes Japan itself doesn’t release sales numbers. The figures that I use for the iTunes chart every week come from an aggregate chart that is posted daily. The source for these charts has now released their year end iTunes single chart for 2016. The period covered is 12/24/15 – 12/23/16. RADWIMPS topped the chart with the movie version of “Zen Zen Zense”, followed by Utada Hikaru’s “Hanataba wo Kimi ni.” RADWIMPS appeared again to round out the top 3, this time with the movie version of “Nandemonai ya.”

1. RADWIMPS – Zen Zen Zense (movie ver.)
2. Utada Hikaru – Hanataba wo Kimi ni
3. RADWIMPS – Nandemonai ya (movie ver.)
4. Hoshino Gen – Koi
5. ONE OK ROCK – Wherever you are
6. Urashima Taro (Kiritani Kenta) – Umi no Koe
7. Hoshino Gen – SUN
8. RADWIMPS – Sparkle (movie ver.)
9. Namie Amuro – Hero
10. RADIO FISH – PERFECT HUMAN
11. Nishino Kana – Torisetsu
12. Utada Hikaru – Michi
13. RADWIMPS  – Yume Tourou
14. Perfume – FLASH
15. Ken Hirai – Mahoutte Itte Ii Kana?
16. Ketsumeishi – Tomo yo~Kono Saki mo Zutto…
17. Fujiwara Sakura – Soup
18. AKB48  – 365 Nichi no Kamihikouki
19. Namie Amuro – Mint
20. Flower  – Yasashisa de Afureru You ni

The rest of the top 300 can be found here.