Infection with the parasitic nematode Strongyloides stercoralis is characteristic for tropical and subtropical regions of the world, but autochthonous cases have been reported in European countries as well. Here we present the first nation-wide survey of S. stercoralis seroprevalence in Croatian individuals presenting with eosinophilia, and evaluate the fraction of positive microscopy rates in stool specimens of seropositive individuals. In our sample of 1407 patients tested between 2018 and 2021, the overall prevalence of strongyloidiasis was 9.31%, with significantly higher rates in those older than 60 years of age (P = 0.005). Of those, one-quarter (25.95%) were also positive following microscopy examination of faeces after using the merthiolate–iodine–formaldehyde concentration method. Our findings reinforce the notion of endemic strongyloidiasis transmission in Croatia, particularly in older individuals, and highlight the need to consider the presence of S. stercoralis in patients with eosinophilia.