Cancer poses a world-wide healthcare problem, demanding selective and effective therapy protocols. To address that, a vast amount of therapeutic candidates are being investigated in the field of medicinal chemistry. Accordingly, indole-benzimidazole structures have recently gained considerable interest because of their anticancer properties and estrogen receptor (ER) modulatory actions. In this study, novel methylsulfonyl indole-benzimidazole derivatives have been synthesized upon substitution of respectively the first (R1) and fifth (R2) positions of benzimidazole and indole groups. Structure and activity relationships were then studied via1H NMR, 13C NMR, mass spectral and in silico docking analyses, as well as cell viability measurements. We found that the compounds exhibited substantial affinity levels towards ER alpha (ERα). In addition, the correlation analysis of cytotoxicity profiles between ethyl- and methyl-sulfonyl indole-benzimidazoles revealed a collection of effective and consistent R1 and R2 substitutions. However, for some candidate derivatives, distinctive cytotoxicity levels and varying viability versus ERα affinity correlations were observable across the studies, suggesting that the sulfonyl side chain modifications themselves can also influence the ERα binding levels. These results demonstrated that our novel methylsulfonyl indole-benzimidazole derivatives, similar to their ethylsulfonyl counterparts, exhibit anticancer effects with potential estrogen receptor modulatory actions.