The 20-year-old Swedish national was detained at a demonstration near the InterContinental Hotel in Mayfair on 17 October as oil executives met inside.
She pleaded not guilty at Westminster Magistrates' Court to breaching Section 14 of the Public Order Act 1986.
Four other Fossil Free London activists pleaded not guilty alongside her.
Ms Thunberg confirmed her name and date of birth, but her address in Stockholm was not read out in court due to concerns over threats she is said to have received.
The protesters were granted unconditional bail ahead of a trial at City of London Magistrates' Court, which is set to start on 1 February.
A group of Greenpeace and Fossil Free London protesters gathered outside Westminster Magistrates' Court, chanting and holding banners reading "oily money out" and "make polluters pay".
A large crowd of photographers and video journalists waited for Ms Thunberg and surrounded her as she left the court.
After failing to break free from the cluster as she walked down the pavement, Ms Thunberg sharply changed direction and sprinted away down Marylebone Road.
The Metropolitan Police had imposed imposed conditions on the 17 October protest under Section 14 of the Public Order Act to "prevent serious disruption to the community, hotel and guests".
Dozens of protesters blocked Hamilton Place, near Park Lane, on the first day of the three-day Energy Intelligence Forum - formerly called the Oil and Money conference - where bosses of Shell and Total were due to speak.
Activists carried banners and pink umbrellas with eyes painted on, shouting "cancel the conference", while some lit yellow and pink flares.
The Met Police previously said a number of protesters failed to move from the road and on to the pavement when asked to do so, resulting in multiple arrests.
Climate campaigner Greta Thunberg has appeared before magistrates to deny a public order offence after her arrest at a protest in central London.