Strongyloides stercoralis, a pathogenic roundworm, is considered endemic in several tropical and subtropical areas worldwide. Indigenous populations have the highest soil-transmitted helminthiases-related mortality rates, but the prevalence and risk factors associated with S. stercoralis in Brazilian indigenous populations have not been established. Thus, the present study aimed to assess the seroprevalence and associated risk factors for S. stercoralis in indigenous communities and the healthcare professionals serving them in Brazil. Indigenous populations living in nine communities and healthcare professionals were tested for anti- S. stercoralis antibodies by ELISA. A questionnaire was used to assess socio-epidemiological information. Associated risk factors for seropositivity were tested by chi-square or Fisher’s exact tests, using bivariate analyses and multivariate logistic regression. Overall, 174/463 (37.6%; CI 95%: 33.3–42.1) indigenous persons and 77/147 (52.4%; 95% CI: 44.3–60.3) healthcare professionals were seropositive for anti- S. stercoralis antibodies. Seropositivity among the two groups was statistically significant (p = 0.0016; OR = 0.547; 95% CI: 0.376–0.796) and revealed that healthcare professionals were 1.83 times more likely to be seropositive. The multivariate analysis showed that being male or being adult were also risk factors, while having a septic tank as a sanitary facility represented a protective factor for S. stercoralis exposure in indigenous persons. None of the variables evaluated were associated with S. stercoralis exposure in the professional group. The study herein has reported a high seroprevalence to Strongyloides stercoralis in indigenous communities of Brazil and healthcare professionals, warning for potential public health concerns of strongyloidiasis in such populations.