Passengers and crew had alerted the pilots that a boy was seen running to the plane as it was taxiing to take off from southern Benin City, Arik Airline spokesman Ola Adebanji said.
The pilots alerted the country's aviation agency.
The incident highlighted growing concerns about airport security in Nigeria, which is fighting an Islamic uprising mainly contained in the north-east of the country, where there is a state of emergency.
Arik Airline managing director Chris Ndulue said: "We are worried by the incessant security lapses at our airports."
Despite the possible presence of the teenager, the pilots opted to continue with their take-off and when the plane arrived in Lagos, a boy aged 13 or 14 jumped to the ground from the wheel and was detained by Arik personnel.