Olga Glamozdinova, who allowed a congregation to gather for weekly worship sessions at her house in the southern village of Veselyi said the decision violated her rights to freedom of religious expression and her right to freely own and dispose of her property.
According to Christian aid agency Barnabas Fund, the church was registered at her property which is built on land designated for "private farming" in January 2017.
Nine months after filing for registration, district officials fined Olga for "use of the land for unintended purposes", a decision that has since been upheld by two court hearings.
Glamozdinova brought her appeal to the Russian Constitutional Court earlier this month.
Under Russian law it is not permitted to register existing residential buildings as churches, but as permission to construct church buildings for Protestant congregations is rarely granted it leaves many with no other alternative.
This legislative contradiction is placing churches under an increasing threat of closure from the authorities.
Glamozdinova lawyer, Vladimir Riakhovsky, said her case exposes a "legal ambiguity" being used to stifle freedom of conscience and religious associations, and argued he had at least a dozen other examples of cases where land designation had been used to restrict the rights of Protestant Christians.
"The right of a religious organisation to conduct worship services in residential buildings is explicitly provided by the Federal Law," he said.
A final decision by the Constitutional Court is expected within the next few months.
If Glamozdinova is successful in appealing the fine it will have significant implications for religious freedom in Russia.
Christian leaders in the Russian port city of Novorossiysk are legally challenging the recent shutdown of a local Baptist Church, describing the closure as a "flagrant violation" of the 1997 Religion Law which prohibits government interference in religion, and establishes simple registration procedures for religious groups.
They have said they are prepared to take the case to the European Court of Human Rights as it "prevents believers from coming together to profess their faith."
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.