A rapid and efficient division is key for the ability of apicomplexan parasites to proliferate and therefore is crucial for their pathogenesis. During the Toxoplasma gondii tachyzoite cell cycle, division and segregation of organelles is a highly coordinated process that ensures that each daughter parasite is properly complemented with all organelles. This highly regulated mechanism implies a tight regulation of gene expression that is crucial for the production of daughter cells in this parasite. However, which proteins are key actors in this regulation remain to be discovered. We discovered that TgAP2IX-5 is a cell-cycle-dependent ApiAP2 transcription factor (TF) bearing a crucial regulatory role during the tachyzoite cell cycle.TgAP2IX-5 also acts as a master regulator that controls the expression of other TFs that may be essential for the completion of the cell cycle. TgAP2IX-5 directly controls the expression of TgAP2XII-9 (Gissot M, Nat Comm. 2021). Nevertheless, the putative TFs' role in the biology of T. gondii has not been studied. To investigate the role of TgAP2XII-9, we produced conditional knock-down strain and characterized its phenotypes. TgAP2XII-9 is essential for the growth of parasites indicating that it may exert essential roles during the cell cycle. We have shown that TgAP2XII-9 localizes to the nucleus and is expressed during the S/M phase in line with its transcript expression profile. Depletion of TgAP2XII-9 causes significant defects in the formation of the daughter cells inner membrane complex therefore producing a significant number of multinucleated parasites. Our CUT&Tag and RNA-seq data unveiled AP2XII-9's direct control over genes including other AP2 TFs, IMC coding genes, and notably, microneme and rhoptry coding genes. There is a strong correlation in these results with the phenotypes observed by investigating cell-cycle markers by IFA with clear IMC and daughter cell formation defects. Surprisingly, most of the genes that are found in both the RNA-seq and CUT&Tag datasets are upregulated suggesting that AP2XII-9 is a repressor of gene expression that controls the cell cycle of T. gondii. To our knowledge, this is the first description of a transcriptional repressor with a direct role in the tachyzoite cell cycle.