A second boat carrying a larger group was scheduled to leave the island later in the morning, state TV reported.
Those who left early on Friday were from Pakistan, it said.
The first group of 202 migrants to be returned, most of them from Pakistan and Afghanistan, were sent back to Turkey on Monday, according to Reuters.
Under the EU-Turkey deal, Ankara will take back all migrants and refugees, including Syrians, who enter Greece through irregular routes in return for the EU taking in thousands of Syrian refugees directly from Turkey and rewarding it with more money, early visa-free travel and progress in its EU membership negotiations.