We report the experimental observation of sublattice-resolved resonant scattering in bilayer graphene by performing simultaneous cryogenic atomic hydrogen doping and electron transport measurements in an ultrahigh vacuum. This allows us to monitor the hydrogen adsorption on the different sublattices of bilayer graphene without atomic-scale microscopy. Specifically, we detect two distinct resonant scattering peaks in the gate-dependent resistance, which evolve as a function of the atomic hydrogen dosage. Theoretical calculations show that one of the peaks originates from resonant scattering by hydrogen adatoms on the a sublattice (dimer site) while the other originates from hydrogen adatoms on the beta sublattice (nondimer site), thereby enabling a method for characterizing the relative sublattice occupancy via transport measurements. Utilizing this new capability, we investigate the adsorption and thermal desorption of hydrogen adatoms via controlled annealing and conclude that hydrogen adsorption on the beta sublattice is energetically favored. Through site-selective desorption from the alpha sublattice, we realize hydrogen doping with adatoms primarily on a single sublattice, which is highly desired for generating ferromagnetism.