Januarius was born in the Caserta Palace, two years before the death of his father Ferdinand II, the penultimate King of the Two Sicilies. At the time of the Prince's birth, Ferdinand was already ill and too weak to play with his youngest son as he had done with his previous eleven children. The young Prince would never know of the carefree experience of growing up in the opulence of the Neapolitan court.

In 1860, the Royal Family of the Two Sicilies was driven from Naples and from the kingdom by Giuseppe Garibaldi and his Expedition of the Thousand. Garibaldi and his troops deprived Januarius and his family of their properties and wealth forcing the family and their descendants into a financially strained and nomadic existence. Pope Pius IX offered the family a residence at Quirinal Palace in Rome as gratitude for their loyalty.

In 1867, a cholera epidemic forced the population, or at least those who could, to leave the capital. Januarius's mother Maria Theresa took the children who still lived with her at Quirinal Palace and moved them over the Alban Hills to Albano Laziale. Despite his mother's efforts to spare her children from illness, the small Januarius contracted cholera. Januarius died almost immediately. Maria Theresa was also infected and died after atrocious suffering, having refused treatment from a doctor whom she considered to be "liberal."