Abstract The Colorado Ultraviolet Transit Experiment (CUTE) is a 6U NASA CubeSat carrying on-board a low-resolution, near-ultraviolet (2479–3306 Å) spectrograph. It has a Cassegrain telescope with a rectangular primary to maximize the collecting area, given the shape of the satellite bus, and an aberration correcting grating to improve the image quality, and thus spectral resolution. CUTE, launched on the of 2021 September 27th to a Low Earth Orbit, is designed to monitor transiting extra-solar planets orbiting bright, nearby stars to improve our understanding of planet atmospheric escape and star-planet interaction processes. We present here the CUTE autONomous daTa ReductiOn pipeLine, developed for reducing CUTE data. The pipeline has been structured with a modular approach, which also considers scalability and adaptability to other missions carrying on-board a long-slit spectrograph. The CUTE data simulator has been used to generate synthetic observations used for developing and testing the pipeline functionalities. The pipeline has been tested and updated employing flight data obtained during commissioning and initial science operations of the mission.