Bird migration has long been hypothesized as the main mechanism for long‐distance dispersal of flaviviruses, but the role of migratory birds in flaviviruses spillover is not well documented. In this study, we investigated the eco‐epidemiology of West Nile virus (WNV) and Usutu virus (USUV) in trans‐Saharan passerines during their spring stopover in southern Tunisian oases. To do, we combined oral swab analysis and serological tools to assess whether migratory birds could be reaching these stopover sites while infectious or have been previously exposed to viruses. All sampled birds tested negative for oral swab analysis. However, anti‐WNV and anti‐USUV antibodies were detected in 32% and 1% of tested birds, respectively. Among WNV‐seropositive species, the Golden oriole (Oriolus oriolus) showed the highest anti‐WNV occurrence probability. In this species, anti‐WNV occurrence was twice larger in males than females. Inter‐specific and intraspecific morphological, physiological and behavioural differences could explain these results. Although our findings did not show evidence for passerines migrating while infectious, they did not exclude an existing enzootic WNV transmission cycle in Tunisian oases. Further investigations including larger samples of migratory birds are needed for a better understanding of this issue.