Alleged international drug dealer Michael Paul Moogan, from Croxteth, Liverpool, has been on the run since a police raid at a Rotterdam cafe in 2013.
The Cafe de Ketel was suspected of being used as a front for meetings between drug traffickers and cartels, and central to an alleged plot to bring hundreds of kilos of cocaine into the UK every week.
The cafe was not open to the public and could only be entered via a security system, the NCA said.
Mr Moogan used numerous false identities and attempted to avoid CCTV to elude capture, the agency added.
The 35-year-old was held on 21 April after a join operation between the National Crime Agency (NCA) and Dubai police, but news of the arrest was delayed for operational reasons.
At the time of the cafe raid, only one of the suspects, Robert Hamilton, 71, from Manchester, could be found. He was jailed for eight years in 2014 after pleading guilty to drug charges.
Another man, Robert Stephen Gerrard, 57, from Liverpool, handed himself in to the NCA after three years on the run, claiming the pressure was too much.
Following Mr Moogan's arrest, NCA Director of Investigations Nikki Holland said: "This arrest is the result of years of investigation involving a range of law enforcement partners in the UK, Europe and Middle East.
"We are extremely grateful to those partners for their assistance in ensuring Moogan now faces justice and particularly thank the Dubai Police for their efforts to track him down.
"He will be returned to the United Kingdom to face trial.
"This case should serve as a warning to others on the run from the NCA - we have a global reach, we never give up and they can never rest easy."
NCA Director General (Operations) Steve Rodhouse added: "The arrest of Moogan further reflects great co-operation between the Dubai Police and the NCA.
"I'd like to commend their work, in particular detectives from the General Department of Criminal Investigation in Dubai, who showed exceptional professionalism and were able to use all the techniques at their disposal to locate him and carry out this operation."