As it stands, the state must grant marriage licenses for same-sex couples starting Oct. 21. But the administration of Christie, a Republican who is considered a possible presidential candidate for 2016, was expected to appeal the denial of the stay to a higher court.
"Granting a stay would simply allow the state to continue to violate the equal protection rights of New Jersey same-sex couples, which can hardly be considered a public interest," Judge Mary Jacobson wrote.
The Christie administration had already asked the state Supreme Court to weigh in Jacobson's initial decision last month that the state had to allow gay marriage.
In her order Thursday, she ruled that the start of nuptials did not have to be delayed, finding the state was not likely to win its appeal and that it would not hurt the state if same-sex marriage licenses are issued.
Gay couples who want to wed "would suffer many hardships of constitutional magnitude if the stay were to be issued, but the state has not demonstrated how it would suffer in any meaningful way if the order is enforced," she wrote.
Thirteen states, including most in the Northeast, already allow gay couples to marry. New Jersey offers gay couples civil unions but not marriage.
The matter has been fought in New Jersey's courts and Legislature for a decade.
"The court's decision once again confirms that the hardships of not being able to marry are real and immediate. Every day does count," said Hayley Gorenberg of Lambda Legal, which had filed a brief in support of same-sex couples seeking the right to marry.
Jacobson's ruling in September concluded that it's unconstitutional for New Jersey to block gay marriage now that the federal government is giving married gay couples legal benefits.
New Jersey's attorney general had argued unsuccessfully that a state law cannot be found unconstitutional because of a change in federal policy.
Gay rights groups are also pushing lawmakers to override Christie's veto last year of a law that would have allowed gay marriage.