Investigators said the child appeared to be around seven-years-old and, judging by the body's advanced state of decomposition, had been dead for several weeks.
The police were called to the property on Tuesday when the owner of the apartment, who had called demanding overdue rent payments, had heard loud shouts from the residence despite there being no response to her ringing of the doorbell.
When the police arrived, witnesses said that the couple were visibly agitated although they did not resist arrest.
Sources close to the case said that there were no obvious signs of violence to the boy.
The same sources also said the suspects are a middle-class family - the father is an engineer - with two other children.
They had been living in Girona for around a year and a half, but the children were not attending a school and hardly ever left the apartment.