| # | Weekend End Date | Film | Total Weekend Gross | Notes |
| 1 | January 1, 2006 | Harry Potter and the Goblet of Fire | $11,445,783 | |
| 2 | January 8, 2006 | Otoko-tachi no Yamato | $9,334,091 | |
| 3 | January 15, 2006 | The Uchōten Hotel | $11,756,367 | |
| 4 | January 22, 2006 | Flightplan | $15,667,919 | |
| 5 | January 29, 2006 | The Uchōten Hotel | $12,178,850 | |
| 6 | February 5, 2006 | $11,391,971 | |
| 7 | February 12, 2006 | Munich | $1,271,448 | |
| 8 | February 19, 2006 | The Uchōten Hotel | $2,064,713 | |
| 9 | February 26, 2006 | Forbidden Siren | $13,902,173 | |
| 10 | March 5, 2006 | The Chronicles of Narnia: The Lion, the Witch and the Wardrobe | $19,064,852 | |
| 11 | March 12, 2006 | $16,269,316 | |
| 12 | March 19, 2006 | $12,242,394 | |
| 13 | March 26, 2006 | $10,131,801 | |
| 14 | April 2, 2006 | $11,089,430 | |
| 15 | April 9, 2006 | $6,967,179 | |
| 16 | April 16, 2006 | Detective Conan: The Private Eye's Requiem | $13,249,896 | |
| 17 | April 23, 2006 | $10,544,636 | |
| 18 | April 30, 2006 | $10,009,176 | |
| 19 | May 7, 2006 | Limit of Love: Umizaru | $17,938,624 | |
| 20 | May 14, 2006 | $12,826,246 | |
| 21 | May 21, 2006 | The Da Vinci Code | $20,074,324 | |
| 22 | May 28, 2006 | $19,370,484 | |
| 23 | June 4, 2006 | $15,998,437 | |
| 24 | June 11, 2006 | $15,755,530 | |
| 25 | June 18, 2006 | Death Note | $16,026,737 | |
| 26 | June 25, 2006 | $12,730,940 | |
| 27 | July 2, 2006 | Cars | $13,394,878 | |
| 28 | July 9, 2006 | Mission: Impossible III | $17,753,945 | |
| 29 | July 16, 2006 | Nihon Igai Zenbu Chinbotsu | $18,401,267 | |
| 30 | July 23, 2006 | Pirates of the Caribbean: Dead Man's Chest | $28,718,560 | |
| 31 | July 30, 2006 | Tales from Earthsea | $22,244,951 | |
| 32 | August 6, 2006 | $18,329,749 | |
| 33 | August 13, 2006 | Pirates of the Caribbean: Dead Man's Chest | $17,524,925 | |
| 34 | August 20, 2006 | Superman Returns | $15,418,008 | |
| 35 | August 27, 2006 | Tales from Earthsea | $11,670,140 | |
| 36 | September 3, 2006 | Miami Vice | $9,806,877 | |
| 37 | September 10, 2006 | X-Men: The Last Stand | $8,967,132 | |
| 38 | September 17, 2006 | The Fast and the Furious: Tokyo Drift | $10,674,273 | |
| 39 | September 24, 2006 | The Lake House | $8,289,150 | |
| 40 | October 1, 2006 | Nada so so | $9,762,445 | |
| 41 | October 8, 2006 | World Trade Center | $9,820,646 | |
| 42 | October 15, 2006 | $7,746,502 | |
| 43 | October 22, 2006 | Nada so so | $7,162,688 | |
| 44 | October 29, 2006 | Kisarazu Cat's Eye | $9,317,220 | |
| 45 | November 5, 2006 | Death Note 2: The Last Name | $13,747,043 | |
| 46 | November 12, 2006 | $10,394,163 | |
| 47 | November 19, 2006 | $10,517,980 | |
| 48 | November 26, 2006 | The Devil Wears Prada | $8,009,899 | |
| 49 | December 3, 2006 | Love and Honor | $10,169,017 | |
| 50 | December 10, 2006 | Letters from Iwo Jima | $13,698,930 | |
| 51 | December 17, 2006 | $15,079,177 | |
| 52 | December 24, 2006 | $12,935,476 | |
| 53 | December 31, 2006 | $6,865,760 | |
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