The news has raised concern that pregnant women are not being vaccinated against the contagious bacterial infection that can be especially deadly in new born babies.
The two-and-a-half month old infant died in Madrid's 12 de Octubre hospital on October 24th although the news was not made public until Wedneday.
Another baby, just 44 days old, is currently hospitalized in Toledo suffering whooping cough, which spreads easily by coughing and sneezing and mainly affects the respiratory system.
On Tuesday it emerged that a baby less than two-months-old in Seville died from whopping cough in September, just days after a two-week-old baby died in Malaga.
Babies are not usually given immunization against whooping cough until they reach two months old, but pregnant mothers are advised to be vaccinated in the final trimester as they can pass on antibodies to their newborns to protect them in the first few months of life.
But the mother of the Malaga baby complained that she had not been able to purchase the vaccine in pharmacies despite it being recommended by her obstetrician.
It has emerged that many regional health authorities in Spain have not been immunizing pregnant women because of a dearth of global vaccinations against pertussis, which can cause pneumonia, seizures, brain damage, and death and is particularly dangerous for young babies.
Only seven of Spain's semi-autonomous regions currently include recommendations that pregnant women are vaccinated, although Andalucia, Aragon, the Balearic Islands and Murcia have all announced that they will introduce the scheme in 2016.
Castilla-La Mancha began vaccinating pregnant women on November 9th as a result of the rise in the number of recent cases.
Spain has seen the number of whooping cough cases soar this year, with 7,224 record so far in 2015 compared with 2,870 in the whole of 2014, reported Spanish newspaper ABC.
Hemos comprado 60.000 dosis de vacunas de tosferina para tener garantías de que disponemos de stock suficiente https://t.co/mvsCn3o2SO— Alfonso Alonso (@AlfonsoAlonsoPP) November 18, 2015
Spain's Minister of Health Alfonso Alonso said on Wednesday that Spain had ordered 60,000 doses of vaccine against whooping cough to address shortages.