Jamie Acourt, 41, from south London, is wanted for alleged involvement in the large-scale supply of drugs, the NCA said.
Acourt is a former suspect in the Stephen Lawrence murder inquiry — a killing that triggered far-reaching changes to British attitudes and policing.
Prince Harry and his fiancee Meghan Markle attended a memorial on Monday marking the 25th anniversary of the racist murder of the black teenager, who was stabbed to death at a south London bus stop in 1993.
Jamie Acourt was never tried in the Lawrence case and has always maintained his innocence.
He was detained on a European Arrest Warrant as he left a Barcelona gym.
He had been due to appear in court in Madrid this week, but at a weekend hearing of the Spanish High Court it was accepted that he will not challenge his extradition.
“Acourt thought he could evade capture but as a result of an intelligence-led operation his days on the run have ended,” said Ian Cruxton, the NCA's international operations chief.
“We were able to direct the Spanish authorities to his location in Barcelona.
“Our ability to share information and work at speed with our international partners ensures there is no safe haven for fugitives. We will never stop pursuing these individuals.”
One of Britain’s most wanted fugitives, Jamie Acourt, was captured in Barcelona today following a joint operation with @metpoliceuk and Spanish National Police.
— NationalCrimeAgency (@NCA_UK) May 4, 2018
The NCA said he was the was the 81st fugitive to be located out of 96 publicised through Operation Captura, which targets Britain's most wanted in Spain.
London's Metropolitan Police said in a statement that the arrest related to a 2016 investigation.
A spokeswoman for the National Crime Agency (NCA) said: “We can confirm that he is not challenging his extradition.”
The NCA could not confirm when Acourt, who remains in custody in Barcelona after appearing in court via videolink, will be brought back to the UK.