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Providing an accurate, representative sample of mass flux across large open areas for atmospheric studies or the extreme conditions of a hypersonic engine is challenging for traditional intrusive or point-based sensors. Here, we demonstrate that laser absorption spectroscopy with mode-locked frequency combs can simultaneously measure all of the components of mass flux (velocity, temperature, pressure, and species mole fraction) with low uncertainty, spatial resolution corresponding to the laser line of sight, and no supplemental sensor readings. The low uncertainty is provided by the broad spectral bandwidth, high resolution, and extremely well-known and controlled frequency axis of stabilized, mode-locked frequency combs. We demonstrate these capabilities using dual frequency comb spectroscopy (DCS) in the isolator of a ground-test supersonic propulsion engine at Wright-Patterson Air Force Base. The mass flux measurements are consistent within 3.6% of the facility-level engine air supply values. A vertical scan of the laser beams in the isolator measures the spatially resolved mass flux, which is compared with computational fluid dynamics simulations. A rigorous uncertainty analysis demonstrates a instrument uncertainty of ~0.4%, and total uncertainty (including non-instrument sources) of ~7% for mass flux measurements. These measurements demonstrate DCS with mode-locked frequency combs as a low-uncertainty mass flux sensor for a variety of applications.