Macsen Oatway from Neath has LAD1, a condition which affects his immune system and is so rare only 400 people in the world have it.
He spent weeks at a specialist isolation unit known as a "bubble" in Newcastle.
Only doctors, nurses and his parents were allowed in.
He received a series of blood transfusions, chemotherapy and a bone marrow treatment - without which Macsen would have had to take antibiotics for the rest of his life.
His parents Richard and Zoe said the treatment "transformed" Macsen's life, and are calling for more people to register on the bone marrow transplant list so any other child born with the condition can live a full life.
Mr Oatway said: "It's so important. You may never get called, but if you do get the opportunity, take it with both hands.
"It's a fantastic opportunity to save a life and to whoever donated to Macsen, thank you very, very much."
Doctors have said Macsen is now well enough to attend school, and his parents said he "loves it".
A three-year-old boy with a rare condition who had to live in a "bubble" to prevent infections during his treatment has started school.