Marine plastic abundance has increased over the past 60 years and microplastics (< 5 mm) constitute a primary component of such litter. Filter-feeding megafauna, such as the whale shark, might be particularly affected by microplastic pollution as their feeding mode requires filtration of up to thousands of cubic meters of water. In addition, the habitat range of whale sharks intersects with several recognized microplastic pollution hotspots, among which is the Coral Triangle. Direct evidence for microplastic ingestion in whale sharks however, has not yet been presented. Here we show that whale shark scat collected in the Philippines from 2012 to 2019 contained a mean of 2.8 microplastics g− 1. Contrary to our expectations, the microplastic concentration in the scat remained consistent from 2012 to 2019. Water samples from the study site in 2019 indicated that the local microplastic pollution (5.83 particles m− 3) was higher than in surface waters in other whale shark habitats, but well below other pollution hot-spots found in Southeast Asia and China (range: 100–4100 particles m− 3). With the predicted growth in plastic use, leading to increased plastic marine pollution, whale sharks are expected to become more exposed to this form of pollution. To what extent microplastic ingestion impacts the overall health status of this endangered species remains an open question.