The body of the boy, identified as Afghan by aid groups, was found in a boat that landed on the island of Chios, the coastguard said.
His family were among 600 migrants who arrived on the island on Wednesday, the day after the government inaugurated a registration facility to regulate the influx to Greece's eastern Aegean islands after over 800,000 people fleeing war and poverty landed there last year.
Lesbos gas seen another 1,076 people arrive since Tuesday, after Greek authorities said the flow had dropped from around 2,500 arrivals per day to 200.
"There has been a slight pick-up in arrivals," a coastguard source said.
Turkey is hosting 2.5 million refugees from Syria's civil war and hundreds of thousands from Iraq, and is increasingly bitter that it has been left to shoulder the burden.
Over 300 people have already died in the crossing this year according to the International Organisation for Migration.
