Abstract Molecular hydrogen is the most abundant molecule in the galaxy and plays important roles in planets, their circumstellar environments, and many of their host stars. We have confirmed the presence of molecular hydrogen in the AU Mic system using high-resolution FUV spectra from HST-STIS during both quiescence and a flare. AU Mic is a ∼23 Myr M dwarf that hosts a debris disk and at least two planets. We estimate the temperature of the gas at 1000–2000 K, consistent with previous detections. Based on the radial velocities and widths of the H₂ line profiles and the response of the H₂ lines to a stellar flare, the H₂ line emission is likely produced in the star, rather than in the disk or the planet. However, the temperature of this gas is significantly below the temperature of the photosphere (∼3650 K) and the predicted temperature of its starspots (≳2650 K). We discuss the possibility of colder starspots or a cold layer in the photosphere of a pre-main-sequence M dwarf.