A novel water compatible thermally stable molecularly imprinted polymer (MIP) was synthesized with bi‐functional monomers such as methacrylic acid (MAA) and 4‐vinyl pyridine (4VP) in the presence of mixed porogens such as THF and toluene for selectively higher adsorption of potential genotoxic compound Bisphenol‐A (BPA) compared to other structurally comparable phenolic compounds from aqueous solution at pH 7.0. The specific adsorption capacity (56.58 mg/g) and selectivity for BPA compared to non imprinted polymer (NIP) (44.10 mg/g) were achieved at 298 K under optimized conditions. The mesoporous imprints in the macroporous polymeric structure, higher pore volume, higher surface area, synergistic effect of H‐bonding, van der Waals force and π‐π interaction in bi‐functional cavities of MIP improved the recognition selectivity of BPA compared to NIP. The comparison of experimental adsorption isotherm with sixteen adsorption isotherm models conferred that the adsorption of BPA on MIP happened to energetically heterogeneous sites of the imprinted polymer through a spontaneous exothermic process. The kinetics of adsorption of BPA by MIP was best modeled via non‐linear pseudo‐second order kinetics. That novel MIP was found to be reusable for several cycles. This is the first report of the synthesis of thermally stable and mesoporous MAA‐4VP bi‐functional bulk MIPs having excellent selectivity, rapid binding kinetics and appropriate adsorption capacity for adsorption of BPA in water.