Climate change can aggravate air pollution, with important public health and environmental consequences. While major sources of uncertainty in climate change projections—greenhouse gas emissions scenario, model response, and internal variability—have been investigated extensively, their propagation to estimates of air quality impacts has not been systematically assessed. Here, we compare these uncertainties using a coupled modeling framework that includes a human activity model, an Earth system model of intermediate complexity, and a global atmospheric chemistry model. Uncertainties in projections of U.S. air quality under 21st century climate change are quantified based on a climate-chemistry ensemble that includes multiple initializations, representations of climate sensitivity, and climate policy scenarios, under constant air pollution emissions. We find that climate-related uncertainties are comparable at mid-century, making it difficult to distinguish the impact of variations in greenhouse gas emissions on ozone and particulate matter pollution. While greenhouse gas emissions scenario eventually becomes the dominant uncertainty based on the scenarios considered, all sources of uncertainty are significant through the end of the century. The results provide insights into intrinsically different uncertainties in projections of air pollution impacts and the potential for large ensembles to better capture them.