In a landmark ruling for gay rights in this deeply Catholic country, the constitutional court condemned the routine denial of residency permits for the spouses of gay citizens who married abroad.
The practice, it said, was discriminatory and a breach of human dignity.
"The refusal to issue permits cannot be based only on gender identity or sexual orientation," it said.
Vladimir Simonko, head of the Lithuanian Gay League, hailed it as "a progressive ruling that sends an important message to our LGBT community and politicians.
"I hope it will lead towards more positive attitude towards gay families," Simonko told AFP.
The migration department said it would change the practice and start issuing permits for same-sex spouses.
Lithuania's constitution defines marriage as a union between a man and a woman.
The heavily Catholic nation of 2.8 million people denies legal recognition to same-sex partnerships.
Reacting to the ruling, Lithuania's Catholic Bishops' Conference criticised the court for what it said was the introduction of a "new legal category" of same-sex families.
"The postulate that the family concept is gender-neutral is not in line with the teachings of the Church," it said.
"Marriage is the basis of the family and it is concluded upon the free mutual consent of a man and woman," it said in a statement.
More than two dozen countries worldwide have enacted legislation to allow same-sex union, with the majority of them being in western Europe, according to Pew Research Centre.