After reading medical reports of the alleged victim, Judge Conal Gibbons said the injuries were too serious to be dealt with in the Dublin District Court.
He ordered the case be sent back to State prosecutors before a decision on whether Stokes will have to stand trial in Ireland's higher Circuit Court.
The Ireland and Celtic striker, 25, who was in the court in central Dublin dressed in a navy suit, white shirt and navy polka dot tie, will have to wait another seven weeks before hearing the fate of his case.
Judge Gibbons said he was refusing jurisdiction in his court - effectively recommending a higher court take on the case.
"If these are the injuries the injured party sustained, to my mind this is not a suitable court," he said.
The judge added: "As a matter of fact it is not a minor offence."
Stokes was accompanied in the courtroom by his father John Stokes.
Judge Gibbons said the Director of Public Prosecutions will have to review the case and come back before the court.
Stokes was remanded on bail until July 17.
The footballer, with an address in the West End of Glasgow, was arrested by appointment earlier this year and charged with assault causing harm to Anthony Bradley, 42, at Buck Whaley's nightclub on Leeson Street, Dublin, on June 8, 2013.
The court heard he made no reply to the charge when it was formally put to him.
He was granted bail on his own bond of 1,000 euro (£814) with no cash lodgement required.
The incident is alleged to have happened last June, several hours after an international between Ireland and the Faroe Islands at the Aviva Stadium.
Mr Bradley, an Elvis impersonator from Ballyfermot, west Dublin, was treated for a suspected broken nose and chipped teeth following an incident in the nightclub.