The acetic acid-catalyzed reaction between 5-chloroisatin and 4-methylthiosemicarbazide yields the title compound, C₁₀H₉ClN₄OS (I) (common name: 5-chloroisatin-4-methylthiosemicarbazone). The molecule is nearly planar (r.m.s. deviation = 0.047 Å for all non-H atoms), with a maximum deviation of 0.089 (1) Å for the O atom. An S(6) ring motif formed by an intramolecular N—H...O hydrogen bond is observed. In the crystal, molecules are linked by N—H...O hydrogen bonds, forming chains propagating along the a-axis direction. The chains are linked by N—H...S hydrogen bonds, forming a three-dimensional supramolecular structure. The three-dimensional framework is reinforced by C—H...π interactions. The absolute structure of the molecule in the crystal was determined by resonant scattering [Flack parameter = 0.006 (9)]. The crystal structure of the same compound, measured at 100 K, has been reported on previously [Qasem Ali et al. (2012). Acta Cryst. E68, o964–o965]. The Hirshfeld surface analysis indicates that the most important contributions for the crystal packing are the H...H (23.1%), H...C (18.4%), H...Cl (13.7%), H...S (12.0%) and H...O (11.3%) interactions. A molecular docking evaluation of the title compound with the ribonucleoside diphosphate reductase (RDR) enzyme was carried out. The title compound (I) and the active site of the selected enzyme show Cl...H—C(LYS140), Cg(aromatic ring)...H—C(SER71), H...O—C(GLU200) and Fe^III...O...Fe^III intermolecular interactions, which suggests a solid theoretical structure–activity relationship.