It comes as the firm attempts to boost its image after its 737 Max plane was grounded last year following two fatal crashes that killed 346 people.
The flight took off near Seattle and lasted four hours. Two attempts were called off this week due to high winds.
Further tests are needed before the aircraft enters service with Emirates next year.
The 252-foot-long passenger plane had been due to launch this year but has been delayed by some technical difficulties.
The 777X is a larger and more efficient version of Boeing's successful 777 mini-jumbo. Standout features include folding wingtips and the world's largest commercial engines.
"It represents the great things we can do as a company," said 777X marketing director Wendy Sowers.
Boeing says it has sold 309 of the plane - worth more than $442 million each at list prices.
The plane will go head-to-head with the Airbus A350-1000 which seats about 360 passengers.