Flight EK0863 from Muscat was grounded after baggage handlers found the serpent in the cargo hold.
A spokesperson for the airline, quoted by Dubai-based media, said the snake was found before passengers boarded the plane.
The aircraft was searched before re-entering service and arriving at its destination several hours later.
Emirates did not specify the species of snake, nor whether it was potentially dangerous.
Comparisons with the 2006 Samuel L Jackson thriller Snakes on a Plane, which sees passengers battle hundreds of highly poisonous snakes in mid-flight, inevitably emerged on social media.
But it's far from the first time a snake has tried to travel free of charge on planes from warm climates.
In November last year, passengers on a Mexico domestic flight were panicked by the appearance of a metre-long snake which dropped from the overhead compartments.
A 10ft (3m) scrub python was spotted clinging on to the wing as a plane made its way between the Australian town of Cairns and Port Moresby in Papua New Guinea in 2013.
And in 2012, animal protection officers had to rescue a young Middle American smooth-scaled racer which arrived in Scotland on a flight from Mexico.
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