Census guidance states

5.2.9 Pupil gender [ALL schools]

The gender of the pupil in the format of ‘M’ (Male) or ‘F’ (Female).

In exceptional circumstances, a school may be unsure as to which gender should be recorded for a particular pupil. Where this occurs, gender is recorded according to the wishes of the pupil and / or parent. 

 

Equal rights guidance offers the following example

1. A previously female pupil has started to live as a boy and has adopted a male name. Does the school have to use this name and refer to the pupil as a boy?
   Not using the pupil’s chosen name merely because the pupil has changed gender would be direct gender reassignment discrimination. Not referring to this pupil as a boy would also result in direct gender reassignment discrimination. 

Please be aware that gender reassignment may cause problems when importing a CTF from a former school and we would always advise the school to take guidance from their MAT or LA

 

Further reading https://www.equalityhumanrights.com/sites/default/files/technical_guidance_for_schools_england.pdf