The 30 minute programme called Just A Girl details the story of an 11-year-old girl named Amy, who reveals she was originally born as a boy called Ben.
Amy depicts the struggles of wanting a sex change at such a young age, with the show looking at themes such as bullying and friendship as well as what it means to be transgender.
The fictional character has chosen to start taking hormones that will stop puberty, making it easier to have a sex change in the future.
The programme is freely available to anyone of any age on the CBBC website.
Parents have expressed their outrage on Mumsnet, claiming that the programme is inappropriate and the young audience is becoming unnecessarily confused.
One mum wrote that her daughter was becoming worried about her own gender, questioning her 'anxiously, if that means she was a boy'.
Peter Bone, a Conservative MP, has also spoken out about the show, saying, 'It beggars belief that the BBC is making this programme freely available to children as young as six. I entirely share the anger of parents who just want to let children be children.
'It is completely inappropriate for such material to be on the CBBC website and I shall be writing to BBC bosses to demand they take it down as soon as possible.'
However, some parents have expressed their support for how the BBC are raising awareness in children. A Mumsnet user has written, 'I don't believe there is "too young" for stuff like this. The earlier you teach your children that everyone is different and that nobody is "normal" the better.'
A spokesperson for the BBC has defended the programme, saying, 'Just A Girl is about a fictional transgender character trying to make sense of the world, deal with bullying and work out how to keep her friends, which are universal themes that many children relate to, and which has had a positive response from our audience.
'CBBC aims to reflect true life, providing content that mirrors the lives of as many UK children as possible.'
Do you think that 11 is too young to learn about transgender issues? Would you let your child watch Just A Girl? Tell us in the comment box below!