Ultrathin amorphous Bi films, patterned with a nanohoneycomb array of holes, can exhibit an insulating phase with transport dominated by the incoherent motion of Cooper pairs (CP) of electrons between localized states. Here, we show that the magnetoresistance (MR) of this Cooper pair insulator (CPI) phase is positive and grows exponentially with decreasing temperature T, for T well below the pair formation temperature. It peaks at a field estimated to be sufficient to break the pairs and then decreases monotonically into a regime in which the film resistance assumes the T dependence appropriate for weakly localized single electron transport. We discuss how these results support proposals that the large MR peaks in other unpatterned, ultrathin film systems disclose a CPI phase and provide new insight into the CP localization.