An 11-week-old boy died from meningococcal septicaemia at the Duchess of Kent Military Hospital in Catterick Garrison, North Yorkshire, on Monday.
Jessica Murdoch, 16 months, died from the same infection in February.
Both fathers are believed to be soldiers in the Royal Irish Regiment but they do not know each other.
Tests are being conducted to establish whether the strains in the two cases are similar and if the deaths are linked.
Dr Phil Kirby, communicable disease consultant for North Yorkshire Health Authority, said: "It is unbelievably tragic for these two families.
"Almost all cases of meningococcal infection are single and isolated, and spread from person to person is rare, even in families or in those having close contact with someone with the disease."
National and regional meningitis specialists have been briefed about the deaths.Reuse content