Almost 24,000 nationals aged 17 to 35 were turned back at the border between January 2014 and March this year, the Nigerian Immigration Service (NIS) told AFP.
"There have been reports in recent times of some Nigerians departing to join terrorist groups especially in the Middle East and north Africa," said NIS spokesman Chukwuemeka Obua.
The crackdown sought to prevent young Nigerians being "lured into terrorism, prostitution, slavery and other untoward activities abroad", the NIS said in a statement.
But the country has also become a "catchment area for recruiters" abroad because of high unemployment, the NIS said.
Among the most high-profile Nigerians convicted for overseas terror offences is 28-year-old Umar Farouk Abdulmutalab, a failed suicide attacker with connections to Al-Qaeda, popularly referred to as the "Underwear Bomber".
He was hailed as a hero by Al-Qaeda chief Osama Bin Laden after trying to blow up a Northwest Airlines flight from Amsterdam to Detroit, Michigan, on Christmas Day 2009 and is serving four life terms in the United States.
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