Studies examining the later-life health consequences of in-utero exposure to influenza have typically estimated effects on physical health conditions, with little evidence of effects on mental health outcomes or mortality. Previous studies have also relied primarily on reduced-form estimates of the effects of exposure to influenza pandemics, meaning they are unlikely to recover effects of influenza exposure at an individual- level. This paper uses inverse probability of treatment weighting and “doubly-robust” methods alongside rare mother-reported data on in-utero influenza exposure to estimate the individual-level effect of in-utero influenza exposure on mental health and mortality risk throughout childhood and adulthood. We find that in-utero exposure to influenza is associated with small reductions in mental health in mid-childhood, driven by increases in internalising symptoms, and increases in depressive symptoms in mid- life for males. There is also evidence that in-utero influenza exposure is associated with substantial increases in mortality, although these effects are primarily driven by a 75% increase in the probability of being stillborn, with limited evidence of additional survival disadvantages at later ages. The potential for mortality selection implies that estimated effects on mental health outcomes are likely to represent a lower bound.