Perceived stigma and organizational barriers to care (stigma/BTC) can influence the decision to seek help for military personnel when they are suffering from mental health problems. We examined the relationship between stigmatizing beliefs, perceived BTC, and probable post-traumatic stress disorder (PTSD) in 23,101 UK military personnel deployed to Afghanistan and Iraq both during and after deployment; and in a smaller group some six months later. Overall, our results suggest that stigma/BTC perceptions were significantly, and substantially higher during deployment than when personnel are returning home; however, within the smaller follow-up group, the rates climbed significantly over the first six-months post-deployment although they still remained lower than during-deployment levels. Male personnel, those who reported higher levels of PTSD symptoms and/or greater combat exposure were significantly more likely to endorse more stigma/BTC at both sampling points. Rates of stigma/BTC on deployment are substantially higher than rates measured when personnel are in less threatening environments. We suggest that the considerable efforts that military forces make to encourage effective help seeking should take account of the fluctuating levels of stigma/BTC. Commanders should be aware that encouraging help seeking may be more difficult in operational environments than when personnel have returned home.