The child was unconscious and having difficulty breathing when paramedics arrived at his Val-Bélair home around 6:30 p.m. Sunday.
He was taken to the medical centre at Laval University where he is recovering.
GHB "duplicates the effect of alcohol. It's very dangerous, especially for a little kid of three years old," Quebec City police spokeswoman Catherine Viel told CBC News.
Police arrested the child’s aunt and father. The father had been living with his sister for around a month.
Youth protection services have also been contacted.
The father and aunt were later released by police on a promise to appear in court.
Police are looking into how the child ingested the dangerous liquid drug, but Viel said police do know that it was accidental.