The teacher, only identified by her first name, Alevtina, was sacked because her employer said her behaviour was incompatible with her job.
Several teachers lost their jobs around the same time in St Petersburg, after being outed by the activist, but Alevtina was the only one to take her challenge to court.
Ksenia Kirichenko, the lawyer for the gay rights group representing the teacher told the press that the court refused to rule in the teacher’s favour.
Kirichenko also said the teacher plans to appeal the ruling, in order to be reinstated.
Gay people have faced increasing issues in Russia since President Vladimir Putin in 2013 signed a federal law banning the “promotion of non-tradtional sexual relations”.