Airborne electromagnetic (AEM) and magnetic survey data were collected during November and December 2016 along 4,212 line-kilometers over Yellowstone National Park, Wyoming. The survey was conducted as part of a study of the subsurface geologic structure and geothermal and groundwater resources of Yellowstone National Park. The survey was designed to image the subsurface plumbing of Yellowstone's myriad thermal features by constraining the geometry of the major hydrostratigraphic contacts and mapping regional-scale geologic structures. Data were acquired by SkyTEM ApS with the SkyTEM 312M time-domain helicopter-borne electromagnetic system together with a Geometrics G822A cesium vapor magnetometer. The survey was flown along six block-style line groups with a nominal line spacing of 450 meters (m), one block-style line group with a nominal line spacing of 250 m, two block-style line groups with a nominal line spacing of 150 m, and a series of regional reconnaissance lines with 5 kilometer (km) nominal line spacing. Due to terrain complexity, the mean flight height was about 48 m. The AEM depth of investigation varies considerably with subsurface resistivity; however, the maximum depth of investigation is about 700 m. This data release includes manually processed AEM data from production flights and inverted models. A shapefile of the AEM flightlines and minimally processed (raw) AEM data supplied by SkyTem Aps are available at https://doi.org/10.5066/P9MCJ9B6.