In recent years, Germany and Austria have been among the leading European receiving countries for asylum seekers and refugees (AS&R). The two countries have cultural and economic similarities, but differ, for example, in their health care systems, with AS&R having unrestricted access to health services upon arrival in Austria, but not in Germany. This study investigates the determinants of health among refugees in Austria and Germany, and how these determinants differ between the two countries. We analyze comparable and harmonized survey data from both countries for Syrian, Afghan, and Iraqi nationals aged 18 to 59 years who had immigrated between 2013 and 2016 (Germany: n = 2,854; Austria: n = 374). The study adopts a cross-sectional design, and uses propensity score matching to examine comparable AS&R in the two receiving countries. The results reveal that the AS&R in Germany (72%) were significantly less likely to report being in (very) good health than their peers in Austria (89%). Age and education had large impacts on health, whereas the effects of length of stay and length of asylum process were smaller. Compositional differences in terms of age, sex, nationality, education, and partnership situation explained the country differences only in part. After applying propensity score matching to adjust for structural differences and to assess non-confounded country effects, the probability of reporting (very) good health was still 12 percentage points lower in Germany than in Austria. We conclude that many of the determinants of health among AS&R correspond to those in the non-migrant population, and thus call for the implementation of similar health policies. The health disadvantage found among the AS&R in Germany suggests that removing their initially restricted access to health care may improve their health.