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