Aims. This study aims to determine the size, albedo, and rotational period of (98943) 2001 CC21, a target of the Hayabusa2 extended mission, using thermal data from the Spitzer Space telescope and ground-based observations.Methods. The Spitzer data were acquired with the Infrared Spectrograph in the 6–38 μm range, reduced using the Spitzer pipeline, and modeled with the near-Earth asteroid thermal model to determine the asteroid size and albedo. The absolute magnitude and rotational period were determined thanks to new observations carried out at the 3.5 m New Technology Telescope, the 1.2 m Observatoire de Haute Provence, and the 0.7 m Abastumani telescope. Three complete light curves were obtained in 2023 and 2024 at the last-mentioned telescope.Results. We determine an absolute magnitude of H = 18.94 ± 0.05 and a rotational period of 5.02124±0.00001 hours, with a large light curve amplitude of ∼0.8 mag. at a phase angle of 22°, indicating a very elongated shape with an estimated a/b semiaxis ratio ≥1.7, or a close-contact binary body. The emissivity of 2001 CC21 is consistent with that of silicates, and its albedo is 21.6±1.6%. Finally, the spherical-equivalent diameter of 2001 CC21 is 465±15 m.Conclusions. The albedo value and emissivity determined here, coupled with results from polarimetry and spectroscopy from the literature, confirm that 2001 CC21 is an S-complex asteroid, and not an L-type one as was previously suggested. The size of 2001 CC21 is less than 500 m, which is smaller than its first size estimation (∼700 m). These results are relevant in preparation of the observing strategy for 2001 CC21 of the Hayabusa2 extended mission.