Protest organizers Extinction Rebellion had vowed to occupy the airport's terminal and shut down operations for three days as part of its action in the British capital.
A London City Airport spokesperson said: "We can confirm that a booked passenger that climbed on top of an aircraft at London City Airport has been removed".
But people have pointed out the "reckless" and "self-serving" nature of the airport protest after Extinction Rebellion tweeted its plans.
18,000 passengers are due to arrive or depart from the airport, with 286 flights scheduled.
London City is the capital's fifth-biggest - and most central - airport, popular with business travellers, bankers and politicians for short-haul and regional routes.
LBC reporter Rachael Venables was at London City Airport as police put up security outside the airport, meaning no one could get into the airport without a boarding pass.More news: Watch Zion Williamson Throw Down Devastating One-Handed Dunk In Debut
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Extinction Rebellion had announced it was planning a "Hong Kong-style" occupation of London City Airport because of the small hub's ongoing expansion plans.
"We continue to work closely with the Metropolitan Police to ensure the safe operation of the airport, which remains fully open and operational".
An activist from Extinction Rebellion in a protest during the group's "Spring Rebellion" in Melbourne on Thursday. "That system will break, as climate chaos hits", group spokesman Rupert Read said in a statement.
The Labour leader spoke out after demonstrations in the capital and other parts of the United Kingdom escalated into a three-day Hong Kong-style protest.
Police said that they had arrested one person on a flight on the runway with a number of people arrested outside the airport, without specifying how many.
Extinction Rebellion has carried out multiple rallies as part of a two-week global campaign. Many commenters are criticizing Extinction Rebellion for potentially endangering lives with their increasingly elaborate stunts, with others saying that climbing on top of a plane is "far beyond acceptable" behavior.