In this paper, we theoretically and experimentally study the performance of an entanglement-based quantum key distribution (QKD) system using single-photon detectors (SPDs) with poor afterpulse characteristics. We reveal that the afterpulse fraction (Pa) in an SPD does not impose a bound on the lowest limit of the error rate in sifted keys of an entanglement-based QKD system. Secure secret key sharing is possible even when Pa is large, for example, exceeding 100%. The system performance in terms of the final key rate is found to be dominated by the parameter η/(1 + Pa) of the SPD, where η is the detection efficiency. The operation conditions of the SPD should be optimized so as to have the maximal η/(1 + Pa), while retaining sufficiently low dark counts. The experimental results were in good agreement with the theoretical predictions. A visibility of 90%, which is sufficiently high for secure secret key sharing in a QKD protocol, was obtained in twofold interference experiments even by using an SPD with Pa exceeding 100%.