Coccidioidomycosis is an emerging fungal infection caused by inhalation ofCoccidioidesspp. spores. While airborne dispersal is critical toCoccidioidestransmission, limited recovery of the pathogen from air has hindered understanding of the aerosolization and transport of spores. Here, we examine uncrewed aircraft systems (UAS) with portable, active air samplers as a novel means of capturing aerosolizedCoccidioidesand characterizing emissions and exposure risk. We sampled in September 2023 in eastern San Luis Obispo County, California, in an area with confirmedCoccidioides immitisin soils. We completed 41 20-minute flights across 14 sites using UAS equipped with an 8 L/min bioaerosol sampler and a low-cost particulate matter sensor. We sampled source soils and air under ambient conditions using one UAS at 1-10 m altitude, and under a simulated high-dust event using two UAS, one at <2 m altitude and one at 5-12 m. We detectedCoccidioidesDNA in two of 41 air samples (4.9%), both under ambient conditions at 8 m altitude, representing the highest known altitude of airborneCoccidioidesdetection. Spatially explicit UAS-based sampling could enhance understanding ofCoccidioidesaerobiology and enable detection in hard-to-reach or hazardous air masses, including dust storms and wildland fire smoke.