The body of the baby boy, estimated to be 6-12 months old, was found dressed in green trousers and white t-shirt on the beach of a hotel.
According to Greek media reports, authorities believe the child belonged was a member part of a migrant family that tried to reach Kos in a dinghy. The body was transfered to Kos General Hospital for an autopsy.
Read: Migrant child's body on beach shocks Europe
The grim discovery recalls the case of three-year-old Syrian boy Aylan Kurdi whose body was found face down on a Turkish beach last month.
Shocking images of that boy's lifeless body helped spur European nations to seek an effective response to the growing migrant crisis.
The Greek Coast Guard continues the grim job of recovering bodies from the sea and the shores of its islands, fearing that things will only get worse as winter approaches and the weather deteriorates.
In September, at least 15 babies and children drowned when their overcrowded boat capsized in high winds off the Aegean island of Farmakonisi.
Around 630,000 people have entered the European Union illegally so far this year, the head of the bloc's border agency said in an interview with French media due to appear Monday.
Over 310,000 of the migrants have landed in Greece, according to UN refugee agency figures. Nearly 3,000 others have died or disappeared during the crossing.
Read: Family of Syrian toddler on Turkish beach tried to reach Canada: report
According to a Frankfurter Allgemeine Sonntagszeitung report on Sunday, the European Union and Turkey have agreed in principle to a plan of action to help ease the flow of migrants into the bloc
Under the plan, Turkey would agree to stepped-up efforts to secure its frontier with the EU by taking part in joint patrols with the Greek coastguard in the eastern Aegean coordinated by EU border protection agency Frontex.
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