On 4 February 1750, Maria Theresa gave birth to a daughter named Maria Joanna Gabriella Josepha Antonia. She was the 11th child and 9th daughter of Maria Theresa and Francis. She was born at the Hofburg Palace.
She spent her childhood in the Kindskammer (imperial nursery) with her large family. From the age of 5, she received her own rooms in the palace. She was particularly close to her sister Maria Josepha. She received an excellent education with a wide range of subjects from the age of three. She loved music and often gave musical performances.
Despite her young age, Maria Johanna was betrothed to the future King Ferdinand III of Sicily and IV of Naples who had been betrothed to her sister Maria Amalia, but that engagement was broken off due to a five year age difference. Maria Johanna was just one year older than her new fiancée.
After her brother, Charles Joseph died of smallpox her mother had her remaining children inoculated. Although all her siblings had no problems with the inoculation, Maria Johanna fell ill. She died a short while later on 23 December 1762. She was still only 12 years old. She was buried in the Imperial Crypt in Vienna.
Maria Theresa undoubtedly had her children inoculated with the smallpox virus obtained from the lesions of extant patients , hence rendering them more likely to acquire the virulent fatal disease as did Charles Josef and Maria Josefa. William Jenner who is credited with the development of the safe form of inoculation used cowpox a more benign form of the virus conferring immunity without the risk of death.