Washington Edison Prado had tried to avoid extradition by claiming he was a member of the Revolutionary Armed Forces of Colombia (FARC) - a status that would have made him eligible for a type of amnesty under a peace deal. Prado was escorted by 50 commandos and agents of various police agencies as he was handed over to the US authorities.
Police say Prado, also known by the alias "Gerald", ran the most sophisticated smuggling route on the Pacific coast of South America.
They compared it to Pablo Escobar's Medellin cartel of three decades ago because it sought to dominate the entire cocaine supply chain from production to its distribution in the US.
Police say Prado and his gang sent as many as 10 speedboats a week that each carried around a ton of cocaine.
It is alleged that Prado began as a boatman running drugs along Ecuador's coast and rose to become head of a small army of smugglers spread across five countries.
Police said that in Ecuador he had records for drug trafficking, migrant smuggling and murder and is accused of ordering attacks against judges, prosecutors and police officers who were investigating him.