Louisa Hodkin, 23, was at the High Court flanked by her fiance as her QC, Lord Lester, attacked the refusal of the Registrar General of Births, Deaths and Marriages to allow the church's chapel in Queen Victoria Street, London, to be used for marriage ceremonies.
The registrar had declined to recognise the chapel as a "place of worship" - the necessary step before marriages can be solemnised - compelling Ms Hodkin to look elsewhere for her wedding venue.
Ms Hodkin is engaged to a fellow scientologist. Lord Lester said her own brother had been allowed to marry at a Church of Scientology chapel in Edinburgh five years ago, a right which was permitted under Scottish law but denied south of the border.
"She and her fiancee both volunteer at the Church of Scientology and seek to celebrate their marriage through a legally recognised scientology wedding, surrounded by their friends, families and fellow volunteers," he added.
The Church of Scientology was founded in 1953 by L Ron Hubbard whose theory of "dianetics" is said to have underpinned its first teachings.
Converts believe individuals have forgotten their true godly natures, which they can rediscover through years of study and meditation and the practice of spiritual "auditing".
Church of Scientology marriages are recognised in a range of different countries, including New Zealand, Canada, the United States and Australia, and church members claim the registrar's refusal is discriminatory and in breach of the 2010 Equality Act.
If the case is successful it would be a victory for the organisation, once described by a British judge as a 'cult', as it seeks political recognition.
Eric Pickles, the Communities Secretary, has previously urged councils not to grant Scientology branches rate relief granted to other religions, saying: "The Church of Scientology is not a registered charity, since the Charity Commission has ruled that it does not provide a public benefit. Nor are its premises a recognised place of worship."
"I do not believe the majority of the public would want their own council to be giving special tax breaks to such a controversial organisation."
The church, whose adherents include actors Tom Cruise and John Travolta, has been accused of mistreating its members.
Lord Lester took the judge, Mr Justice Ouseley, on an extensive trawl through jurisprudence and religious history which he said demonstrated the church's credentials and scientologists' rights to marry in their own places of worship.
He described scientology as a "theistic religion", in company with many of the major world faiths, and insisted that its chapels are used for "worship".
"It is a religion which believes in a supreme being," he told the judge, adding: "As all the evidence before the registrar shows it does so in a profound way."
Scientologists acknowledge the supreme being in their services, in the same way as Roman Catholics or Baptists or Muslims, he said, and so "should be treated the same as those groups".
Some of the church's tenets were similar to those of Buddhists, involving belief in a "cycle of birth and death" and a conviction that "one can realise one's true spiritual identity through spiritual exercise and training, and so eliminate the causes of suffering".
But James Strachan, for the registrar, insisted Miss Hodkin's challenge was "misconceived".
The decision not to recognise the chapel as a marriage venue had been made under the 1855 Places of Worship Registration Act, he said, and was exclusively focused on "whether the place in question is for use for religious worship".
"It is not a conclusion as to whether or not scientology is a religion, or whether it is inherently theistic or otherwise," he told the court, insisting that the "essential ingredients" of religious worship are absent from scientology meetings.
"There is also a sermon in which they listen to a pre-recorded speech by L Ron Hubbard, and then there's a group meeting," he explained.
The legal challenge is being brought by Ms Hodkin and the Church of Scientology Religious Education College Inc.
Outside court, their solicitor, Paul Hewitt, said: "At present, members of the church are not allowed to marry in accordance with their religion in England and Wales and have their marriage given legal recognition, even though they are currently entitled to do so in Scotland and many other common law countries such as Australia, Canada, New Zealand, South Africa and the United States.
"'We hope this case will rectify the position."
The hearing continues.