We investigated the combined effect of melatonin (MEL) and cytarabin (CYT) at a low concentration on acute promyelocytic leukemia cells HL-60. A combined application of these substances led to a decrease in the number of cells by 70% and in the index of mitotic activity, by 75%. A combined effect of MEL and CYT also contributed to a decrease in the expression of mitochondrial proteins. The mitochondrial isoform of VDAC1 can be a target in the treatment of various tumors. A combined application of MEL and CYT at a low concentration (2 nM) reduced the expression of VDAC1. MEL in combination with CYT exerted a similar effect on the expression of the translocator protein (TSPO) and anti-apoptotic protein Bcl-2. The results show that MEL is able to produce a synergistic effect when combined with CYT, thereby increasing the effectiveness of its antitumor action.