Yaneva, who was suspended last week by the Supreme Judicial Council, handed in her resignation late Monday.
Novinite reports that Bogdana Zhelyavska, one of her deputies, will act as interim president until Yaneva is replaced.
Yaneva is accused of abusing her position and approving an unlawful 300-day investigation by the Ministry of the Interior during which officials allegedly wiretapped anti-government protesters.
In December 2014, 15 judges from the Sofia City Court called for Yaneva’s resignation, with the support of seven ambassadors to Bulgaria.