The ECHR said Gareth Lee failed to “exhaust domestic remedies” in the long-running so-called “gay cake” case.
In 2018, the UK Supreme Court ruled Mr Lee was not discriminated against when Ashers bakery in Belfast refused to make him the cake.
Mr Lee then referred the case to the ECHR, claiming the Supreme Court had failed to give appropriate weight to him under the European Convention of Human Rights.
But in a written ruling on Thursday, the ECHR said: “Convention arguments must be raised explicitly or in substance before the domestic authorities.
“The applicant had not invoked his convention rights at any point in the domestic proceedings.
“By relying solely on domestic law, the applicant had deprived the domestic courts of the opportunity to address any convention issues raised, instead asking the court to usurp the role of the domestic courts.
“Because he had failed to exhaust domestic remedies, the application was inadmissible.”
The high-profile controversy first flared when Mr Lee, a member of the LGBT advocacy group QueerSpace, ordered a £36.50 cake from Ashers in May 2014 featuring Sesame Street puppets Bert and Ernie for a private function marking the International Day Against Homophobia.
His order was accepted and he paid in full, but two days later the Christian owners of the company called to say it could not proceed due to the message requested.
Mr Lee then launched the legal case, supported by Northern Ireland’s Equality Commission, alleging discrimination on the grounds of his sexuality. He won hearings at the county court and the Northern Ireland Court of Appeal in 2015 and 2016.
But the owners of Ashers, Daniel and Amy McArthur – backed by the Christian Institute – challenged those rulings at the Supreme Court, and in 2018 five justices unanimously ruled they had not discriminated against the customer.
The Christian Institute welcomed the ECHR ruling, saying it was the “right result”.
Spokesman Simon Calvert said: “The UK Supreme Court engaged at length with the human rights arguments in this case and upheld the McArthurs’ rights to freedom of expression and religion.
“It was disappointing to see another attempt to undermine those rights, so it is a relief that the attempt has failed.
“I’m surprised anyone would want to overturn a ruling that protects gay business owners from being forced to promote views they don’t share, just as much as it protects Christian business owners.
“The ruling in October 2018 by five of the country’s most distinguished and experienced judges was welcomed by lawyers, commentators and free speech experts from across the spectrum.
“They all knew of the implications for freedom of speech and religion, had the decision gone against Ashers.
“This is good news for free speech, good news for Christians and good news for the McArthurs.”