The boat carrying 101 people, including 43 minors and four pregnant women, arrived in Cyprus on Tuesday having set off from Turkey the previous night.
The migrants told police the 22-year-old was the one who steered the boat and he was arrested on Tuesday evening.
The suspect was questioned and said he was approached by an unknown person in a café in Mersin two weeks ago. The man allegedly told him his job was to take people from Turkey to other countries.
When the 22-year-old said he wanted to leave the country himself, the other man replied he had to pay $4,000.
However, he did not have the money.
The man then suggested he and another person could travel for free if he operated the vessel.
The boat had had been spotted by coastal radars at around 11.30am five nautical miles off Cape Greco in Famagusta. Marine police boats were dispatched to the area and accompanied the vessel to a fishing shelter in Protaras for processing.
The passengers were examined for Covid-19 symptoms before they were put on buses that carried them to the reception centre in Kokkinotrimithia.
The pregnant women were taken to hospital as a precaution.
The Syrians had set off from Mersin, having paid from $2,000 to $4,000 each for the trip to Cyprus.