The pair, aged 23 and 27, have also been charged with a number of other serious sexual offences involving both the 12-year-old and another girl aged 15.
It is understood the alleged incidents took place on the Lagan towpath on Monday afternoon.
Appearing together in the dock of Lisburn Magistrates Court on Boxing Day were Gerard Michael Owen McKenna, 27, of Rockville Street in Belfast and Paul Sheridan, 23, unemployed of Hillfoot Crescent in Ballynahinch.
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Both have been charged with the rape of the 12-year-old while McKenna is also accused of three counts of sexual assault by penetration on another girl aged 15.
McKenna, a shop employee, is also accused of stealing alcohol worth £2.99 on December 23, tendering counterfeit currency on December 24 and making threats to kill two men on December 25.
A detective sergeant told District Judge Amanda Henderson that police could connect both men to the charges and had strong objections to bail being granted.
He said further sexual assaults occurred after the two men and the two girls travelled by train to Belfast, after they had acquired alcohol.
The detective confirmed to a defence lawyer that the charges were based on verbal accounts of the incidents as formal statements of complaint had not yet been recorded.
These would be carried out “in the coming days” he said.
McKenna disrupted the proceedings on a number of occasions – challenging the officer’s version of events – and was warned by the judge to desist or face removal from the court.
According to details on the charge sheets, McKenna responded to the rape charge by saying “shove it up your h**e,” and to other charges with the replies “madness” and “not true”.
Sheridan made no reply to the two charges he faced, but a lawyer representing the 23-year-old said his client did not accept the version of events laid out in court.
Refusing bail, Ms Henderson said she shared police concerns regarding bail – stressing “the age and vulnerability of the injured parties” as major factors in her decision.
Both men were remanded to appear back in court via videolink on January 6.