In October, it confirmed to the family no pupil would be allowed to use opposite-sex changing rooms or undress in front of pupils of the opposite sex.
The precise date the practice stopped is unclear.
The father and daughter withdrew their legal challenge ahead of a High Court hearing scheduled for Tuesday.
The father said: “Girls should not have to find out by accident that a biological boy may be using their changing room, and my daughter’s privacy, dignity and safety should never have required a protracted legal battle.
“We trusted Dorothy Stringer to protect her. Instead, our family paid in time, money and emotional strain to secure protections she should have been able to take for granted.”
He added: “Schools must listen to girls and safeguard them. No child’s protection should depend on her family’s ability to fight a legal case.”
Paul Conrathe, of law firm Conrathe Gardner, who represented the family, said: “My clients are delighted. With an utter disregard for safeguarding, the school allowed biological boys into the girls’ changing rooms and toilets on a case-by-case basis for several years, but now they have finally dropped this practice.
“The father’s numerous safeguarding complaints went unheeded and as a result he and his daughter had no choice but to commence proceedings in the High Court to force the school to abandon its unlawful policy.”
The Good Law Project yesterday commented on the withdrawal of the case as a victory, insisting the school had acted lawfully and considered the needs and safety of all pupils.
Today it closed its crowdfunding appeal after raising more than £15,000 to support the school’s defence.
The row also puts the spotlight on Brighton and Hove City Council, which endorsed the case-by-case approach in its controversial “Trans Toolkit” for schools.
It states: “The use of changing rooms by trans children and young people should be assessed on a case-by-case basis in discussion with the individual child or young person.”
That advice is at odds with the new Government rules.
Neither the teenager nor her father can be named for legal reasons.
A spokesman for the school said: “It’s important to note that the claimant withdrew their legal challenge. Our school has always complied with the law, considering the individual circumstances, needs and safety of all students, and we stand behind our commitment to support all of them. We continue to provide facilities that give every pupil the option of privacy and dignity in compliance with statutory guidance.”