"A pregnant woman was infected by Zika and dengue and the foetus has shown various defects," the health authority of the Catalonia region said in a statement.
This was Spain's first case of Zika-related microcephaly, where babies are born with abnormally small heads and sometimes brain damage and thought to be the first case reported in Europe.
A total of 105 people in Spain have been infected with the mosquito-borne Zika virus, according to official statistics from May 3rd.
Spanish authorities have said all the infection cases - including 13 pregnant women - are "imported cases" found in people either "from, or who have visited affected countries" in Latin America.
The current Zika outbreak began in early 2015 in Brazil, where some 1.5 million infections have been reported. Since then, the epidemic has spread to several other countries in the Americas.
Scientists believe the virus to be responsible for a surge in Brazilian infants born with microcephaly.
There is no vaccine or treatment for the virus, which in most people causes only mild symptoms - a rash, joint pain or fever.