New therapies for leukemia are urgently needed due to adverse side effects, tumor resistance and lack of selectivity of many chemotherapeutic agents in clinical use. Ageratum conyzoides has been used in folklore medicine for managing leukemia and other cancers. Thus, this study aimed to investigate the effects of fractions, sub-fractions and purified compounds from the ethanol leaf extracts of A. conyzoides against Jurkat cells-model for acute T cell leukemia. A two-dimensional purification process using normal phase flash, followed by reverse phase purification was necessary to isolate pure methoxy-flavones, which were further characterized by Nuclear Magnetic Resonance (NMR) and MS-MS. The effect of fractions or pure compounds on cell viability was determined using either the MTT reagent or CellTiter-Blue® assay, while the caspase-3 and -7 activation was tested with Caspase-Glo® 3/7 assay. Prediction of compounds' drug disposition profiles in vivo was measured with biomimetic affinity chromatography methodologies.