US Customs and Border Protection (CBP) has advised Qatar Airways it can board travellers from seven Muslim-majority countries and all refugees who had been banned under the order, according to a statement on the Doha-based airline's website.
A spokeswoman confirmed the airline would start accepting all passengers with valid travel documents including a Green Card.
Trump suspended the entry of nationals from Iran, Iraq, Libya, Somalia, Sudan, Syria and Yemen, and all refugees in a controversial order signed on January 27.
The ban caught the airline industry off guard, with some carriers forced to re-roster flight crew in order to abide by the order.
The judge's temporary restraining order represents a major challenge to Trump's action, although his administration could still appeal the ruling and have the policy upheld.
The travel ban, which includes a ban on Syrian refugees being resettled in the US, has sparked international outcry and protests as well as confusion at airports as some travellers were detained.