U.S. District Court Judge J. Campbell Barker, appointed by former President Donald Trump, determined that the program, known as Keeping Families Together, violates U.S. immigration law.
The decision follows a lawsuit filed by Texas and several other Republican-led states.
The ruling marks a significant setback for the Biden administration, which argued that the initiative aimed to support family unity in mixed-status households.
Officials had estimated that about half a million undocumented immigrants could benefit from the program.
The Justice Department may appeal the decision, but with the incoming Trump administration set to take office, it is likely that Biden’s immigration policies will face further rollbacks.
Trump has pledged to strengthen border security and implement mass deportations.
Announced by President Biden in June, the Keeping Families Together program aimed to provide work permits and deportation protections for undocumented immigrants married to U.S. citizens who have lived in the country for at least 10 years without committing serious offenses.
The policy also offered a pathway to permanent residency, allowing eligible immigrants to apply for green cards and eventually citizenship after three years.