In the Daily Mail article the mosque say that they are relying on Section 195 and Schedule 23 paragraph 2 of the Equality Act.
Section 195 deals with sport and allows for single-sex competitions (eg men-only and women-only events) where the activity is "a gender-affected activity". In other words where being stronger, taller etc can make a difference.
This can include things like running, playing football, swimming etc. But it also covers other sports such as, most recently, pool.
There is ongoing debate about at what age young boys start to outperform young girls and so at what age does sport, such as running, become a "gender-affected activity".
It appears that the mosque would likely argue that running is not a gender-affected activity for children aged under 12. However, if you have any 11 year old children then you will have noticed that boys of that age can definitely run faster than girls - on average.
The Schedule 23 part is that they can restrict participation to muslim people only.