Shinjuku held a mayoral election on November 12, 2006. Hiroko Nakayama, backed by the LDP and New Komeito Party was re-elected. Polling turnout was extremely low, only 26% but still about 1% more than last election.
| Party | Candidate | Votes | % | ±% | |
|---|---|---|---|---|---|
| LDP, NKP | Hiroko Nakayama (中山 弘子) | 44,472 | |||
| JCP | Kazu Sueyoshi (末 吉和) | 12,372 | |||
| Independent | Haruji Ishioka (石岡 春二) | 5,168 | |||
| Turnout | 63,079 | 26.58 | 1.43 | ||