The Federal Fiscal Court (BFH) in the southern city of Munich said in a statement that it had ruled in favour of a woman in a civil union with a female partner, each of whom brought two children into the relationship.
German child benefits are granted to parents on a sliding scale with the sum per child increasing for large families.
The plaintiff, who was not identified by the court, argued that she and her partner were entitled to the higher rate of 215 euros ($296) per child per month given to families with four children.
A lower court had dismissed her claim but the federal tribunal found in her favour on the basis of a high court ruling this year requiring tax equality for same-sex couples.
"The BFH decided with its ruling that this legal application was also relevant for determining child benefit rates," it said.
German law has since 2001 allowed civil unions for gay and lesbian couples, granting many but not all the rights extended to heterosexual spouses.
The country's highest court in June ordered tax equality for gay couples in a landmark ruling, following a decision in February which found that gays in a civil union should be allowed to adopt their partners' adopted children.
Gay couples are still forbidden from adopting children together in Germany.
Chancellor Angela Merkel's conservative Christian Democrats on Wednesday entered into formal coalition talks with the country's second biggest party, the Social Democrats, who have said they will fight for an equality provision for same-sex couples in the new government accord.