The arrest of Daniel Burdett, a suspected criminal gang ringleader from Liverpool, "shows that no matter where you are, we will catch up with you", said the agency.
Mr Burdett had been on the run for five years before the authorities caught up with him on Christmas Day at a restaurant in The Hague.
He was detained by Dutch police on a European Arrest Warrant. It allows EU member states to request the arrest and detention of suspected criminals in other countries.
It is believed the 28-year-old uses corrupt lorry drivers to smuggle firearms and ammunition from the Netherlands to the UK.
He is also wanted for drugs offences by Merseyside Police.
Mr Burdett faces 10 charges of conspiracy to import firearms and conspiracy to supply class A and class B drugs.
He will appear before Dutch magistrates who will consider extraditing him to the UK to face the charges.
"The arrest of one of our long-standing fugitives is a fantastic result," said NCA branch commander Mark Spoors.
"Burdett thought he could evade the law by exploiting international borders, but his arrest shows that no matter where you are, we will catch up with you.
'Other fugitives should pay attention'
"Other fugitives should pay attention to this and remember how determined UK law enforcement is," said Mr Spoors.
"Thanks to the co-ordinated response by the Dutch police and Merseyside Police, Burdett is now facing extradition to the UK.
"The public can be assured that the NCA is relentlessly pursuing those suspected of causing the most harm to the UK, even on Christmas Day," he added.
One man has already been jailed for eight years in connection with the investigation and another is currently awaiting trial, according to the NCA.