The ministry says the man is from Yemen and arrived in Spain on Tuesday. A ministry statement gave no other details on the man.
Spain has said it is prepared to take in up to five people from Guantanamo to help the United States in its drive to close the facility.
Spain accepted a Palestinian former inmate, in February.
The ministry statement said the Yemeni, like the Palestinian, met the condition that he does not have charges pending in the U.S., Europe or Yemen. Both men will be able to work in Spain and move around the country freely but cannot leave it.