Due to the unavailability of GPS indoors, various indoor pedestrian positioning approaches have been designed to estimate the position of the user leveraging sensory data measured from inertial measurement units (IMUs) and wireless signal receivers, such as pedestrian dead reckoning (PDR) and received signal strength (RSS) fingerprinting. This study is similar to the previous study in that it estimates the user position by fusing noisy positional information obtained from the PDR and RSS fingerprinting using the Bayes filter in the indoor pedestrian positioning system. However, this study differs from the previous study in that it uses an enhanced state estimation approach based on the ensemble transform Kalman filter (ETKF), called QETKF, as the Bayes filer for the indoor pedestrian positioning instead of the SKPF proposed in the previous study. The QETKF estimates the updated user position by fusing the predicted position by the PDR and the positional measurement estimated by the RSS fingerprinting scheme using the ensemble transformation, whereas the SKPF calculates the updated user position by fusing them using both the unscented transformation (UT) of UKF and the weighting method of PF. In the field of Earth science, the ETKF has been widely used to estimate the state of the atmospheric and ocean models. However, the ETKF algorithm does not consider the model error in the state prediction model; that is, it assumes a perfect model without any model errors. Hence, the error covariance estimated by the ETKF can be systematically underestimated, thereby yielding inaccurate state estimation results due to underweighted observations. The QETKF proposed in this paper is an efficient approach to implementing the ETKF applied to the indoor pedestrian localization system that should consider the model error. Unlike the ETKF, the QETKF can avoid the systematic underestimation of the error covariance by considering the model error in the state prediction model. The main goal of this study is to investigate the feasibility of the pedestrian position estimation for the QETKF in the indoor localization system that uses the PDR and RSS fingerprinting. Pedestrian positioning experiments performed using the indoor localization system implemented on the smartphone in a campus building show that the QETKF can offer more accurate positioning results than the ETKF and other ensemble-based Kalman filters (EBKFs). This indicates that the QETKF has great potential in performing better position estimation with more accurately estimated error covariances for the indoor pedestrian localization system.