This will be the second time that they have removed a child from school after his older brother, 8, also had a boy in his class who wore dresses.
Nigel Rowe, 44 and Sally, 42, plan to challenge the school's approach and are now set to take the Diocese of Portsmouth to court arguing that it has not respected their rights to raise their children with biblical values.
Nigel Rowe stated: "A child aged six would sometimes come to school as a girl or sometimes come to school as a boy. Our concerns were raised when our son came back home from school saying he was confused as to why and how a boy was now a girl.
"We believe it is wrong to encourage very young children to embrace transgenderism. Boys are boys and girls are girls. Gender dysphoria is something we as Christians need to address with love and compassion, but not in the sphere of a primary school environment."
The school, which has not been named, said it had anti-transphobia policies and that children were protected under the Equality Act 2010.
But lawyers for the Rowe family are set to argue that the law only applies to people over 18. They will also argue that the school the school is discriminating against the couple by implying that their wish to bring up their sons with biblical beliefs is transphobic.