Some demonstrators climbed on top of the square's famous fountains as the mostly peaceful group waved flags and banners and let off fireworks on Saturday afternoon.
At least one protester was seen carrying a banner which read "Let's keep the world clean" with a picture of an Israeli flag being thrown into a bin.
A similar banner displayed at a protest in Warsaw was condemned by the Israeli ambassador to Poland as "blatant antisemitism".
Other protesters chanted "from the river to the sea, Palestine will be free", despite controversy around the slogan's meaning.
Home Secretary Suella Braverman has previously branded the slogan antisemitic and claimed that it is "widely understood" to call for the destruction of Israel.
However, pro-Palestinian protesters have contested this definition.
Former Labour leader Jeremy Corbyn and comedian Alexei Sayle were among those who addressed the crowd on a stage set up in the square.
Other speakers led chants of "free, free Palestine" and were cheered by the large crowd which filled the famous square in central London.
Just after 5pm, the Metropolitan Police said 11 people had been arrested .
Protesters also gathered for a sit-in at Charing Cross station, which is near to Trafalgar Square in central London, on Saturday evening .
Earlier in the day, 350 people staged a sit-in protest which shut down Oxford Circus.
The demonstration stopped traffic during the shopping district's busiest hours, following similar disruptive protests at major stations.
It comes after a week of similar disruptive actions at major UK transport hubs.
The Home Secretary has previously caused controversy by describing the demonstrators taking to the streets in support of a ceasefire in Gaza as being involved in "hate marches".
A group of campaigners also gathered outside the Home Office in Westminster in opposition to Ms Braverman's comments on refugees and tents pitched by homeless people in public spaces.