| Rank | LW | Release
| Gross | %± LW | Theaters | Change | Average | Total Gross | Weeks | Distributor
| New This Week
| Estimated
|
|---|
| 1 | 1 | Ponyo | $7,904,102 | +12.7% | 481 | - | $16,432 | $92,309,426 | 5 | Toho | false | false |
| 2 | - | The Mummy: Tomb of the Dragon Emperor | $7,115,345 | - | 548 | - | $12,984 | $7,115,345 | 1 | Toho-Towa | true | false |
| 3 | - | What Happens in Vegas | $1,695,852 | - | 191 | - | $8,878 | $1,695,852 | 1 | 20th Century Fox International | true | false |
| 4 | 3 | Pokémon: Giratina and the Sky Warrior | $1,615,310 | -16.1% | 359 | - | $4,499 | $36,233,144 | 5 | Toho | false | false |
| 5 | 2 | The Dark Knight | $1,613,101 | -47.9% | 460 | +1 | $3,506 | $8,764,176 | 2 | Warner Bros. | false | false |
| 6 | 5 | Boys Over Flowers: Final | $1,278,899 | <0.1% | 316 | - | $4,047 | $64,887,855 | 8 | Toho | false | false |
| 7 | 6 | Kung Fu Panda | $1,093,200 | +2% | 438 | - | $2,495 | $13,480,654 | 4 | Asmik Ace Entertainment | false | false |
| 8 | 4 | Kamen Rider Kiva: King of the Castle in the Demon World | $1,013,353 | -40.4% | 286 | - | $3,543 | $4,929,088 | 2 | Toei Company | false | false |
| 9 | 7 | Naruto Shippuden: The Movie - Bonds | $775,923 | -18.3% | 252 | - | $3,079 | $7,947,209 | 3 | Toho | false | false |
| 10 | 9 | The Sky Crawlers | $453,929 | -24.3% | 213 | - | $2,131 | $4,377,074 | 3 | Warner Bros. | false | false |
| 11 | 8 | The Happening | $407,124 | -40.3% | 309 | - | $1,317 | $10,613,491 | 4 | 20th Century Fox International | false | false |
| 12 | 11 | Kitaro and the Millennium Curse | $402,756 | -2.3% | 311 | - | $1,295 | $11,767,263 | 6 | Shochiku | false | false |
| 13 | 10 | Indiana Jones and the Kingdom of the Crystal Skull | $383,866 | -27.4% | 423 | -171 | $907 | $51,876,953 | 9 | Paramount Pictures International | false | false |
| 14 | 12 | The Forbidden Kingdom | $266,858 | -29.7% | 193 | -4 | $1,382 | $5,920,411 | 4 | Shochiku | false | false |
| 15 | - | Kung Fu Dunk | $154,266 | - | 104 | - | $1,483 | $154,266 | 1 | Herald Film Company | true | false |
| 16 | 14 | Anpanman: The Secret of Fairy Rin-Rin | $113,085 | -8% | 135 | -16 | $837 | $2,869,967 | 6 | Tokyo Theatres | false | false |
| 17 | 13 | The Magic Hour | $102,550 | -28.5% | 212 | -79 | $483 | $35,549,212 | 11 | Toho | false | false |
| 18 | 15 | The Incredible Hulk | $69,255 | -43.2% | 161 | -12 | $430 | $1,431,562 | 3 | Sony Pictures Releasing | false | false |
| 19 | - | One Million Yen Girl 2008 Re-release | $55,778 | - | 20 | - | $2,788 | $1,506,690 | 5 | Nikkatsu | false | false |
| 20 | 17 | Across the Universe | $37,251 | -14.8% | 13 | +2 | $2,865 | $165,324 | 2 | Tohokushinsha Film Corporation (TFC) | false | false |
| 21 | 18 | Still Walking | $26,828 | -9.1% | 15 | - | $1,788 | $1,220,351 | 8 | Cine Quanon | false | false |
| 22 | 19 | The Witch of the West Is Dead | $23,579 | -15.2% | 14 | -5 | $1,684 | $3,914,606 | 9 | Asmik Ace Entertainment | false | false |
| 23 | 22 | Semi-Pro | $12,547 | -31.1% | 5 | - | $2,509 | $68,677 | 2 | Gaga | false | false |
| 24 | - | After School | $8,182 | - | 5 | - | $1,636 | $4,766,629 | 13 | The Klockworx | false | false |
| 25 | 23 | Starship Troopers 3: Marauder | $7,968 | -54.3% | 9 | -7 | $885 | $394,986 | 5 | Sony Pictures Releasing | false | false |
| 26 | 25 | Newcastle | $175 | -34.5% | 1 | - | $175 | $114,017 | 11 | Sony Pictures Releasing | false | false |
| 27 | 24 | Made of Honor | $145 | -99% | 1 | -13 | $145 | $1,293,292 | 6 | Sony Pictures Releasing | false | false |
