Naomi Hayama, 39, had been conducting yoga classes twice a week for the last nine years at the St. Michael and All Angels Church in Bishopston, Bristol.
The priest and the council at the church, however, decided to evict Hayama for practicing an exercise too "spiritual".
Hayama has been given until the end of the month to find a new location for her class.
"They are trying to say it is a spiritual practise but my classes are not. I respect people who are religious but I am not. That's what attracted me to yoga - you don't have to be religious to teach it," said Hayama.
"My students are puzzled and outraged as well. My class is a physical exercise which is about relaxation and breathing and it's a healthy thing to do."
Hayama had a membership of 30 students at the church and teaches a total of 600 students across Bristol.
Despite Hayama collecting over 500 signatures in an effort to convince the church to reconsider their decision, Reverend James Stevenson and the Parish of Bishopston said the church space should only be used for Christian acts of worship.
Meanwhile, Hayama's students have defended the class by saying it has no religious content.
"The decision was made without seeing my class, which is what I have a real problem with. Seeing it and deciding it's not appropriate is one thing but to do no investigation and just talk about yoga's background is another," said Hayama.
Meanwhile Rev Stevenson defended the church's decision and said, reported The Telegraph: "We understand yoga is practiced as a physical exercise and discipline but it's definitely a spiritual act whose roots are not Christ centred.
"One student of the class said everyone he had spoken to had viewed it as a ridiculous decision but every church leader I've spoken to completely understands this decision."