The Personal Status Court of First Instance ruled that the plaintiff had suffered physiologically and psychologically since childhood due to hormonal imbalances, defence lawyer Adil al-Yahya told Reuters on Sunday.
Saturday's ruling has to be referred to a higher court before the decision becomes final, al-Yahya said, adding the process might take up to a month.
Al-Yahya said he presented the court with an edict issued by Egypt's al-Azhar, Sunni Islam's top religious institution, that allowed people to change their gender if medical reports showed this was to their benefit.
"We have evidence, a fatwa from al-Azhar, because we have a case of illness, not a case of switching gender or as they call it in Kuwait a third-sex case," al-Yahya told Reuters. "This is a very rare condition...and the court ruled according to that condition."
The 25-year-old plaintiff, who wants a name change to Amal from Ahmad, had a sex-change operation in Bangkok in October 2002, the Arab Times daily reported.