We report evidence for Milankovitch cycles discovered in Middle Permian strata of the fluvial Abrahamskraal formation, lower Beaufort Group, in Karoo Basin of the Northern Cape Province, South Africa. Statistical analyses of ranked lithologies and of major element oxides have been used to obtain clusters of elements that capture lithological variations and reflect changes of the sedimentary environment through time. Spectral analysis of these elemental statistical groups reveal significant meter-scale sedimentary cycles of 67 m, 17.5 m, 5.9 m and 3.5–2.8 m, which can be interpreted as the sedimentary expression of astronomical forcing, based on the available estimate of sedimentation rate. The identified periods of short-eccentricity, precession and obliquity show a good match with those predicted for Middle Permian times, providing a data-based validation of the astronomical theory. Cycle counting integrated with available UPb dating, provides a cyclochronological calibration for Wordian normal magnetozones and, combined with radiometric ages, indicates an age of 266.5 ± 0.26 Ma for the end of Kiaman superchron. Recognition of the orbitally driven sedimentation in Gondwana supercontinent suggest a global extension of astronomical influence of Permian climate and confirms empirical knowledge of Earth's astronomical parameters before 260 million years ago. The new data demonstrate a rare case of astronomically paced cyclicity in fluvial deposits and a unique cyclostratigraphic record of the Middle Permian Gondwana supercontinent whose sedimentation reflects orbitally-paced precipitation changes. •First report of Milankovitch cycles in Middle Permian strata in the interior of Gondwana supercontinent.•Fluvial sedimentation controlled by orbitally-paced precipitation changes.•Validate empirical knowledge of Earth's astronomical parameters before 260 Ma.•Combined astronomical and radiometric age of the end of the Kiaman superchron.•Cyclostratigraphic calibration of the length of GU1n/r (Wordian) magnetochrons.