The 2006 Thunder Bay municipal election was held on 13 November 2006 in Thunder Bay, Ontario, Canada, to elect a mayor, 12 city councillors, trustees for the Lakehead District School Board, the Thunder Bay Catholic District School Board, the Conseil scolaire de district du Grand Nord de l'Ontario, and the Conseil scolaire de district catholique des Aurores boréales. This election coincided with the 2006 Ontario municipal elections being held across Ontario.

Voters are asked to elect a mayor, five at-large city councillors and seven ward councillors to the Thunder Bay City Council. Of 86,914 registered voters, 33,196 votes were cast and 33,192 votes were counted. Voter turnout was the lowest in the city's history at 38.2%.^[1]

Three candidates ran for the office of mayor. The incumbent, Lynn Peterson, was re-elected by a considerable margin.

Five councillors are elected at-large to sit on City Council. Fifteen people ran for the position in 2006. Each registered voter can choose up to five candidates.

The city of Thunder Bay is divided into seven electoral wards: Current River, McIntyre, McKellar, Neebing, Northwood, Red River, and Westfort.^[2] Residents of each ward elect one member to represent their ward on city council. Twenty people ran for these positions in five wards. The incumbent councillors in Northwood and Neebing wards were acclaimed.

On 18 October 2007 Andy Savela announced his resignation to take on further responsibilities with the Canadian Auto Workers.^[3] City council voted 6–5 on 5 November 2007 to appoint Robert Tuchenhagen, to the position. Tuchenhagen was defeated by Savela by 377 votes. He was sworn in on 19 November 2007.^[4]

The incumbent, Linda Rydholm, was acclaimed.

The incumbent, Mark Bentz, was acclaimed.

Three boards of education to which voters elect trustees operate in the city of Thunder Bay. The Lakehead District School Board is an English language public school board and elects 8 trustees at-large in the Thunder Bay Census Metropolitan Area, the Thunder Bay Catholic District School Board is an English language separate school board and elects 6 trustees at-large in the Thunder Bay Census Metropolitan Area, the Conseil scolaire de district du Grand Nord de l'Ontario is a French language public school board and elects one trustee from Northwestern Ontario, and the Conseil scolaire de district catholique des Aurores boréales is a French language separate school board and elects 4 trustees at-large in Northwestern Ontario.

Eight trustees are elected to the Lakehead District School Board by registered voters in the city of Thunder Bay, the six municipalities in its CMA, and voters in the unorganized portion of Thunder Bay District. Each registered voter can choose up to eight candidates. Thirteen people ran for this position.

Six trustees are elected to the Thunder Bay Catholic District School Board by registered Roman Catholic voters in the city of Thunder Bay, the six municipalities in its CMA, and voters in the unorganized portion of Thunder Bay District. Each registered voter can choose up to six candidates. Fourteen people ran for this position.

One trustee is elected to the Conseil scolaire de district du Grand Nord de l'Ontario by registered voters with French-language education rights in Northwestern Ontario.

Four trustees are elected to the Conseil scolaire de district catholique des Aurores boréales by registered Roman Catholic voters with French-language education rights in Northwestern Ontario. All four candidates, Anne Breton, Angele M. M. Brunelle, Bernard Caron and Claudette Gleeson, were acclaimed.

• Thunder Bay City Council
• 2006 Ontario municipal elections