Within a generic model, we discuss the possibility of coherent control of charge fluxes in unbiased molecular junctions. The control is induced by resonances between the Rabi frequency due to a pumping laser field and internal characteristic frequencies of pre-designed molecular donor-bridge-acceptor complexes. Two models are considered: a coherently controlled molecular charge pump and a molecular switch. The study generalizes previous consideration of light induced current [M. Galperin and A. Nitzan, Phys. Rev. Lett. 95, 206802 (2005)10.1103/PhysRevLett.95.206802] and of a molecular electron pump [R. Volkovich and U. Peskin, Phys. Rev. B 83, 033403 (2011)10.1103/PhysRevB.83.033403] and accounts for the coherently driven charge transport in an unbiased molecular junction with symmetric coupling to leads. Numerical examples demonstrate the feasibility of the control mechanism for realistic junctions parameters.