Judge Robin Tolson dismissed a woman's allegation she had been raped by her then partner, saying she did "nothing physically" to stop him.
The woman argued the judge's approach led to her losing the legal battle with the man, which centred on their son.
Women's Aid told the BBC family courts were not safe spaces for domestic and sexual abuse survivors.
The case had started when the man asked to be allowed to spend time with his son, who was in the care of his former partner. She objected because she said the man had been controlling and had raped her.
A High Court judge has now upheld an appeal made by the woman over the handling of the case and said the other judge had come to a "flawed" verdict.
Ms Justice Russell, based in the Family Division of the High Court in London, said specialist training is needed on how family court judges deal with sexual assault allegations.
In her ruling, she said family court judges often had to make decisions about cases where there had been allegations of serious sexual assault - but they had not always had training on the issue.