Panama's foreign ministry said the service -- which will be the world's longest nonstop flight at 17 and a half hours -- will "strengthen" commercial and cultural ties between the Middle East and Central American hubs.
Underlining this "new era of relations," the foreign minister of the United Arab Emirates, Sheikh Abdullah bin Zayed al-Nahyan, will visit Panama next Thursday to discuss bilateral issues, the ministry said in a statement.
The Emirates flights were meant to have already begun this week. But they were delayed to March 31, reportedly because codeshare agreements with other airlines needed more time.
Signup to our newsletter and follow us on Facebook and Twitter!
Now, though, the spread of the Zika virus through Central America could put a crimp in bookings to Panama.
The World Health Organization suspects the mosquito-borne virus might be behind a spike of birth defects in northern Brazil, and several countries have cautioned about travel to affected destinations.
Emirates, which already flies to Brazil, is reportedly offering refunds or reticketing for passengers with travel booked to such countries.
The airline's plan for servicing Panama is to use Boeing 777s -- aircraft configured for just 266 passengers, around half of what its flagship Airbus A380s can carry.
Emirates, a subsidiary of a holding company wholly owned by Dubai's government, flies to more than 150 destinations. Dubai is now ranked the world's busiest airport in terms of international passenger numbers.