U.S. District Judge Daniel Jordan issued a preliminary injunction Thursday.
In his ruling, he cited the Supreme Court's decision last year that legalizes same-sex marriage
Based on that decision, the Mississippi ban violates the "equal protection clause" of the constitution, according to the judge.
The Supreme Court's decision encompasses benefits associated with same-sex marriages, such as adoption, he said.
"It also seems highly unlikely that the same court that held a state cannot ban gay marriage because it would deny benefits—expressly including the right to adopt—would then conclude that married gay couples can be denied that very same benefit," Jordan wrote.
The Mississippi ban went into effect in 2000. The federal judge ordered the state Department of Human Services to stop enforcing it.
The ruling is in response to a lawsuit last year by four same-sex couples,
along with the Campaign for Southern Equality and the Family Equality Council.
"Mississippi is the only state left in the nation that bans gay couples from adopting," the advocacy groups said at the time.
A series of other states, including Florida and Nebraska, have overturned similar bans in recent years.
Religious freedom bill
Jordan's ruling comes as Mississippi lawmakers are considering
a bill that would allow businesses and religious groups to decide who gets their services.
The religious freedom bill states that organizations should be at liberty to deny LGBT individuals services such as marriage, adoption and foster care.
The bill considers itself as protecting from discrimination anyone who believes marriage is between one man and one woman and the terms male and female pertain only to a person's genetics and anatomy at birth.
Gov. Phil Bryant has not indicated whether he would sign the religious freedom bill, but he has said the proposed legislation is not discriminatory.