The teenager was among four people detained at the demonstration – where activists wore yellow hi-vis jackets, similar to those worn in recent weeks by anti-government protesters in France.
On Westminster Bridge on Saturday, people were seen burning an EU flag and some protesters chanted: “We want Brexit. When do we want it? Now.”
Used smoke bombs were also seen discarded on nearby streets.
Scotland Yard said: “Four arrests have been made following protests on Westminster Bridge, SW1 at approximately 11am today.
“Three men arrested on suspicion of public order offences. A 13-year-old girl was also arrested on suspicion of assault on police.”
The teenage girl was later released under investigation on Saturday night.