At least nine refugees were previously deported from the island, which lies just 100 kilometers off the Syrian coast.
Over 100 refugees, including 42 children, were rescued on Thursday after their boat was found adrift off the northwest coast of Cyprus, local authorities said.
The Larnaca Joint Rescue Coordination Centre (JRCC) had received information on Wednesday evening that the boat carrying about 130 people on board was in danger.
"The passengers spent the night in Polis Chrysochous, and after the necessary medical checks, they will be transferred to the Kokkinotrimithia reception centre in the afternoon," the civil defence spokeswoman Olivia Michaelidou told Cyprus Mail on Thursday.
The boat carrying refugees is believed to have set off from Turkish port of Mersin, police said.
Refugees reportedly said that they paid $2,200 individually to be brought to the island, which lies just 100 kilometres (60 miles) off the Syrian coast.
Authorities noticed during checks that at least nine of the refugees had previously been deported from the island.
The Cyprus Civil Defence released a statement after the rescue operation, saying the physical situation of all on board is good, adding that a woman who gave birth on the boat was hospitalised.
"Upon arrival, a woman and her new-born baby were transferred to Polis Chrysochous hospital. She said she had given birth on the boat. Both the mother and the baby are in good health," Michaelidou said.
Last month, a boat carrying 83 Syrian refugees that departed from Mersin was towed a harbour on the east coast of the island.
The International Organization for Immigration reported on Tuesday that more than 339,783 migrants and refugees have tried to cross the Mediterranean Sea this year and 4,233 of them have died on the way.