A novel molecularly imprinted electrochemical sensor based on Fe3O4 nanobeads immobilized on graphene (Fe3O4-MIP@RGO) has been developed for detecting 17β-estradiol (17β-E2) in water using reversible addition fragmentation chain transfer (RAFT) polymerization technique. 17β-E2 can be detected by this electrochemical sensor through the response current change before and after binding 17β-E2. The Fe3O4-MIP@RGO-based sensor amplifies the response current in differential pulse voltammetry measurement, allowing the detection limit reaching 0.819 nM in a wide linear range from 0.05 to 10 μM. Moreover, Fe3O4-MIP@RGO-based sensor exhibits high selectivity and sensitivity towards 17β-E2. This MIP electrochemical sensor has a promising potential in the detection of 17β-E2 in water.