Objective To prove the molecular mechanisms of Mahkota Dewa (Phaleria macrocarpa) in suppressing proliferation of human retinoblastoma cells through suppression of cell cycle's gene-regulators expression. Methods In this study, the molecular mechanism of anti-tumor effect of fractioned extract of Phaleria macrocarpa (DLBS1425) in human retinoblastoma cells Y-79 was investigated by measuring the tumor cells viability, the assessment of population profiles of tumor cells in the cell cycle, and the mRNA concentration of p16, p21, p53, cyclin D, cyclin E, and E2F. Results DLBS1425 showed an inhibition effects towards proliferation of Y-79 cell line. Inhibition of proliferation was shown by suppression of cell cycle progression. DLBS1425 downregulated cyclin E, a G1 phase regulator gene of cell cycle, in dose-dependent manner without affecting p53–p21 pathway. In the other word, DLBS1425 inhibits cell proliferation through suppression of cyclin E independently towards conventional proliferation pathway. Conclusions Our results suggest that DLBS1425 is a potential anticancer agent which targets genes involved in cell proliferation in human retinoblastoma cells which make it pharmacologically ideal for the prevention and/or treatment of retinoblastoma cancer.