No saturation in the introduction, acceleration of spread and the increasing impacts of alien species are a characteristic feature of the Anthropocene. Concomitantly, alien species affecting human health are supposed to increase, mainly due to increasing global trade and climate change. In this study, we assess challenges and solutions posed by such species to the public health sector in Austria over the next few decades. We did so using an online questionnaire circulated to 131 experts and stakeholders working on human health and biological invasions, supplemented by in-depth interviews with eleven selected experts. Results from the online survey and in-depth interviews largely support and complement each other. Experts and stakeholders suggest that (i) the allergenic Ambrosia artemisiifolia (common ragweed), the photodermatoxic Heracleum mantegazzianum (giant hogweed), and vectors of diseases such as Aedes albopictus (Asian tiger mosquito) are considered the alien species posing the most severe challenges; (ii) challenges are expected to increase in the next few decades and awareness in the public health sector is not sufficient; (iii) effective and efficient solutions are mainly related to prevention. Specific solutions include pathway management of introduction and spread by monitoring and controlling established populations of ragweed, hogweed and mosquitos.