The teen will be remanded in custody and will appear at the Liverpool Magistrates Court on Thursday, the police said.
The 17-year-old was in police custody on suspicion of murder and attempted murder after the bloody rampage on Monday at a "Taylor Swift yoga and dance workshop", a summer vacation event for children aged 6 to 11 in the English seaside town. The three girls killed were aged 6 to 9.
Police said the person charged cannot be named for legal reasons because he is under 18 years of age.
Disturbances in Southport on Tuesday took place after false information was spread on social media that the suspect behind the stabbings was a radical Islamist migrant.
In London on Wednesday, thousands gathered near the prime minister's Downing Street residence, shouting "Save our kids", "We want our country back" and "Stop the boats", as well as English football chants.
Police have said the attack was not terrorism-related and that the suspect was born in Britain, quashing speculation on his origins.
A large number of police wearing helmets formed a barrier around the protesters, who earlier threw flares and smoke canisters towards Downing Street.
The police said in a separate statement that over a 100 people were arrested for offences including violent disorder, assaulting an emergency worker and breaching protest conditions.
Police were braced for further trouble in Southport, where more than 50 officers were injured on Tuesday night in violent clashes. Police vans were set on fire and protesters hurled bricks, bottles and fireworks at officers and cars parked at the town's mosque.
"Just to reassure the communities of Southport, who I am sure are really worried about 'are we going to see this again tonight?' - we are absolutely planning for this evening and for the weekend ahead," Serena Kennedy, chief constable of Merseyside Police, told reporters.
In Monday's attack in the normally quiet town in northwest England, in addition to the three girls killed, eight other children were stabbed. Five remained in critical condition in hospital, along with two adults who tried to protect them.
Police statements that the suspect was born in Britain did not stop protesters, who police believe were supporters of a right-wing, anti-Islam, anti-immigration group, from targeting the Southport mosque and attacking police who tried to stop them.
'THUGS FROM OUT OF TOWN'
Politicians and police said most of those taking part in the violence were not from the area, and that the clashes detracted from a large vigil attended by thousands to pay tribute to the young victims.
Police said 53 officers were hurt, with eight treated in hospital for serious injuries including fractures and head wounds. Three police dogs were also hurt.
The police chief said she was disgusted and appalled by the violence. Four men, aged between 31 and 39, have been arrested and police were seeking to identify others involved.
"They were there purely for hooliganism and thuggery in terms of bringing that level of violence and that behaviour on to the streets of Southport and that is not what this community is about," she said.
Prime Minister Keir Starmer blamed "violent thugs" and said they would "feel the full force of the law".
On Wednesday, streets in Southport were littered with bricks from broken walls, smashed bottles, large garbage bins and their contents. Charred tarmac bore witness to police vehicles set alight a night earlier.
"What I saw last night was absolutely appalling. ... It was devastating and it's kind of taken away from actually what's gone on, which is the tragedy of those deaths," local resident David Burgess told Sky News.
Taylor Swift fans have so far raised more than 270,000 pounds ($346,000) to help families of the victims and for the hospital where some of the children were being treated. ($1 = 0.7795 pounds)
