The other 38 passengers, including a woman who had fallen overboard, were rescued after local fishermen raised the alarm.
Ten of the survivors were taken to hospital to be treated for hypothermia. The rubber vessel had set off from Turkey in the early morning in windy weather.
The toddler's body was pulled out of the water by fishermen, according to the coastguard. The migrants, including the child's mother, were taken to the port of Pythagorio on Samos, the nearest island, which is 50 kilometers away.