Abstract Biodiversity in ecosystems plays an important role in supporting human welfare, including regulating the transmission of infectious diseases. Many of these services are not fully-appreciated due to complex environmental dynamics and lack of baseline data. Multicontinental amphibian decline due to the fungal pathogen Batrachochytrium dendrobatidis (Bd) provides a stark example. Even though amphibians are known to affect natural food webs—including mosquitoes that transmit human diseases—the human health impacts connected to their massive decline have received little attention. Here we leverage a unique ensemble of ecological surveys, satellite data, and newly digitized public health records to show an empirical link between a wave of Bd-driven collapse of amphibians in Costa Rica and Panama and increased human malaria incidence. Subsequent to the estimated date of Bd-driven amphibian decline in each ‘county’ (canton or distrito), we find that malaria cases are significantly elevated for several years. For the six year peak of the estimated effect, the annual expected county-level increase in malaria ranges from 0.76 to 1.1 additional cases per 1000 population. This is a substantial increase given that cases country-wide per 1000 population peaked during the timeframe of our study at approximately 1.5 for Costa Rica and 1.1 for Panama. This previously unidentified impact of biodiversity loss illustrates the often hidden human welfare costs of conservation failures. These findings also show the importance of mitigating international trade-driven spread of similar emergent pathogens like Batrachochytrium salamandrivorans.