The emergency alert happened at the airport in Perpignan, France, which had just arrived from Oran, Algeria.
Passengers were cleared from the plane after it landed just before 2pm local time.
Emergency services than took the child to a hospital to undergo tests.
Others on board were all made to disinfect their hands and their details were taken for monitoring.
Airport staff were given a warning by the medical authorities in Algeria.
It comes after 100 people were taken ill on an Emirates flight from Dubai to New York.
Cholera is an infection of the small intestine – and kills up to 130,000 people every year, with a further 5 million infected.
There was an outbreak of Cholera in Algeria earlier this year – which killed two people.
Health ministry bosses have since insisted the infection is now under control.
Emergency personnel responded to reports of sick passengers aboard an Emirates flight arriving at John F. Kennedy Airport on Wednesday morning. Hazardous materials crews responded to the jetliner just after it landing at 9 a.m. The plane has been quarantined, according to mayor's office.
An airport source told Fox 5 News that a medical emergency happened on the plane.
In a statement, Emirates said that "about" 10 passengers became ill and local health authorities were alerted "as a precaution." But U.S. Centers for Disease Control and Prevention officials responded to the plane to evaluate about 100 of the 521 people aboard Flight EK203 from Dubai who complained of illness, including a cough and a fever.
The plane had stopped in Mecca, which is the midst of a flu outbreak, Fox News reported.
The CDC reportedly examined passengers away from the main terminal to make sure that a possible contagious disease would not spread.
A New York Police Department counterterrorism division tweeted that it was monitoring what appeared to be a "medical situation."
After spending about an hour or more on the tarmac, everyone on the flight filled out CDC paperwork, deplaned individually, and allowed medical personnel to take their temperatures. Then they boarded buses and again waited outside customs for some time before being admitted to the country.
In the end, ambulances carried just three passengers and seven crew members to a hospital, the airline said.
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