Christopher Ahn was arrested and is expected to be arraigned on Friday in federal court in Los Angles, according to a law enforcement official and a source close to the group.
The US Justice Department declined to comment.
In April, investigators said the intruders, self-professed members of a group seeking the overthrow of North Korean leader Kim Jong Un, removed computers and hard drives from the embassy before fleeing to the United States, where they handed the material to the FBI. Sources said the material had been returned by Spanish authorities to Pyongyang's mission.
A group of at least 10 people stormed into the embassy in February, restrained and physically beat some personnel and held them hostage for hours before fleeing, the Spanish court said earlier.
The anti-Kim group, which calls itself Cheolima Civil Defense, said the raid was not an attack and that it had been invited into the embassy.
Three of the intruders took an embassy official into the basement during the raid and encouraged him to defect from North Korea, according to a detailed document made public on March 26 by the Spanish court.The document included the names of the leaders of the group, some of whom are believed to be in the United States, while others could have left for other countries. The court is seeking their extradition.