People at the centre try and help the children come to terms with having been forced to fight.
Sometimes their parents come and visit them on Sundays.
Therapy includes taking part in pretend battles where one side is the LRA, the other the Ugandan army. At the end, the charity Amnesty International comes in and makes peace.
Children can spend up to two months in these centres, based around the country.
Is there anywhere that children are safe at night?
Some hospitals and church halls are opening their doors at night for children to stay there.
What is the rest of the world doing to help?
Other countries around the world are aware of what's happening but so far not much has been done to help.
Last year, the UN said the situation in northern Uganda was worse than anywhere else in the world.
But the government says it's sure their army can defeat the rebels.