It comes just hours after Mr Johnson said it was not “politically correct bunny hugging” to take action to combat climate change.
Swedish climate activist Ms Thunberg removed everything else on her Twitter bio after she added in the new moniker on Thursday.
Previously, it said: “Seriously annoying climate and environmental activist with Asperger’s.”
Earlier on Thursday, Mr Johnson addressed a virtual summit of world leaders aimed at galvanising international action to curb rising global temperatures.
The UK prime minister said: "It’s vital for all of us to show that this is not all about some expensive, politically correct, green act of bunny hugging, or however you want to put it, there’s nothing wrong with bunny hugging.”
He said taking on the climate emergency was about “growth and jobs” and said the US president, Joe Biden, was “right to stress that”.
Mr Johnson added: "We can build back better from this pandemic by building back greener."
Last year, Ms Thunberg changed her Twitter name to “Sharon” after a quiz show contestant guessed the Swedish activist’s name wrong in a question - which ended up in a clip circulated over social media.
On Thursday, the activist warned US politicians history will hold them accountable for climate catastrophes if they do not stop subsidising fossil fuel production, calling tax breaks for the industry a “disgrace.”
The 18-year-old, whose activism has inspired a global movement, testified virtually to a House of Representatives panel on the day Mr Biden began the virtual climate summit pledging to slash US greenhouse gas emissions in half by 2030.
The two-day summit on Earth Day also heard from leaders from major economies including China, Brazil, Russia and India - with countries including Japan and Canada announcing more ambitious goals to cut emissions in the next decade.
Additional reporting by agencies