Pärnu City Council expressed no confidence in mayor Kristel Voltenberg.
Voltenberg said she would resign voluntarily. However, the council still held a vote.
23 members supported the no-confidence motion. Voltenberg was still mayor during the vote.
Voltenberg said: "I will leave gracefully."
Pärnu had not had a mayor removed by no-confidence vote in over 20 years.
The new mayor is Siim Suursilla (Isamaa).