The aerial part of Allium mongolicum Regel (AMR) which is abundant in the southeastern regions of Mongolia, is used as a food spice. When the crude extracts of this plant were prepared and used for the experiments different biological activities were observed because the extracts contained many polar to nonpolar compounds. This study aimed to prepare subfractions from the crude methanolic extract of AMR and to compare their antiproliferative effects on human cancer cells (HepG2, and MCF-7 cells). The methanolic extracts of AMR were fractionated into six subfractions (methanol, hexane, dichloromethane, ethyl acetate, butanol, and water residue) by solvent–solvent partitioning. The total phenolic content (TPC) was measured by the Folin-Ciocalteu assay. The antioxidant activity of the sub-fractions was determined via DPPH⋅ and ABTS⋅+ assays. Subfraction antiproliferative activity on human cancer cells, HepG2 and MCF-7 cells, was determined by MTS assay. Subfractions showed completely distinct antioxidant and antiproliferative activities (p < 0.001). The highest TPC was in the ethyl acetate fraction (165.4 ± 0.5 mg GAE/g), and the TPC following the addition of dichloromethane, butanol, and methanol. The lowest two were in the n-hexane and water residue fractions. The ethyl acetate fraction showed the highest free radical scavenging activity in both the DPPH⋅ and ABTS⋅+ assays (660.0 ± 5.24 µM TE/g dw the DPPH⋅ assay; 312.7 ± 5.6 µM TE/g dw the ABTS⋅+ assay). The dichloromethane subfraction affected HepG2 cell proliferation and reduced viable cancer cells. Additionally, the dichloromethane and hexane subfractions affects MCF-7 cell proliferation by reducing the number of viable cancer cells. Subfraction methanolic extract by solvent partitioning is helpful for identifying biologically active compounds that show antiproliferative activity.