Along with the group Fossil Free London, the Swedish climate activist stood outside the entrance in Canary Wharf on Thursday morning.
They moved to block the entrances of the bank by sitting on the pavement chanting “oily money out” and waving yellow flags and banners.
It follows another protest on Tuesday in Mayfair where oil executives had met as part of the Energy Intelligence Forum, where Ms Thunberg was arrested and subsequently charged with a public order offence.
The group said the bank has been a major source of funding of fossil fuel projects since the Paris Agreement, when governments agreed to limit global average temperature rise to 1.5C above pre-industrial levels.
Fossil Free London campaigner Henry, who declined to give his last name, said: “Since the Paris climate agreement they have been the worst financiers of fossil fuels, having provided 434 billion dollars (£357 billion) in finances.
“They are making billions of profit every year at a time of worsening inequality when so much of the world is being devastated by the climate crisis.
“We think there should be no new fossil fuel investment or financing from JP Morgan and we think that some of their billions of profits should go towards loss and damage to the communities affected by climate change and provide the financing for adaptation and mitigation measures.”
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