Abstract Atomic oxygen is a main component of the mesosphere and lower thermosphere of the Earth, where it governs photochemistry and energy balance and is a tracer for dynamical motions. However, its concentration is extremely difficult to measure with remote sensing techniques since atomic oxygen has few optically active transitions. Current indirect methods involve photochemical models and the results are not always in agreement, particularly when obtained with different instruments. Here we present direct measurements—independent of photochemical models—of the ground state 3 P 1 → 3 P 2 fine-structure transition of atomic oxygen at 4.7448 THz using the German Receiver for Astronomy at Terahertz Frequencies (GREAT) on board the Stratospheric Observatory for Infrared Astronomy (SOFIA). We find that our measurements of the concentration of atomic oxygen agree well with atmospheric models informed by satellite observations. We suggest that this direct observation method may be more accurate than existing indirect methods that rely on photochemical models.