More than 4,000 military members were prevented from traveling to the United States on Saturday due to the travel ban.
But a number of others were allowed to board flights, and others have been allowed to re-enter the country.
The military said it has been issuing travel warnings and issuing travel refunds to all members of the armed forces, including those stationed overseas.
Some of those orders were issued on Friday.
Military members are also required to complete a training course before they can re-enlist in the military, but those instructions were issued late Saturday, the service said in a statement.
The White House said Sunday it would review the new guidance and would decide whether to appeal the decision to the U.S. Court of Appeals for the District of Columbia Circuit.