A.L.
I would not be too concerned about it. I get them every now and then and so do about 20% of all people. Onset is usually in childhood and 3 does not seem too early.
Since someone else mentioned it though... people often confuse canker sores with Herpes (cold sores).
Canker sores (also called aphtae) are ulcerations of the mucous membrane of the mouth. A canker sore on the lip would be on the inside, the side facing his teeth, the "wet part" not on the "dry part" of the lip. It is not quite clear how they occur but they an an inflammatory response and not infections. Canker sores can be recurrent, they are often treated symptomatically just to alleviate the pain/discomfort.
Herpes or cold sores are cause by Herpes Simplex Virus 1 (HSV-1), this is not the same as the chickenpox virus (Varicella Zoster Virus or VZV). They are related but not the same.
Herpes lesions can occur on the skin (usually around the mouth or on the lips) or on mucous membranes (inside the mouth). If they occur on mucous membranes it is very difficult for a layperson to distinguish them from a canker sore. Herpes is contagious and though most infections are mild it can be dangerous for newborns and immunocompromised people. There is no vaccine for HSV-1 but sometimes treatment with antivirals is indicated, especially for people prone to complications.
If you have a newborn in the house or are due to give birth soon you may want to check in with your pediatrician to make sure it's really a canker sore. Otherwise I would not worry.
Good luck.