Indoor positioning systems have attracted much attention with the recent development of location-based services. Although global positioning system (GPS) is a widely accepted and accurate outdoor localization system, there is no such a solution for indoor areas. Therefore, various systems are proposed for the indoor positioning problem. Fingerprint-based positioning is one of the widely used methods in this area. WiFi-received signal strength (RSS) is a frequently used signal type for the fingerprint-based positioning system. Since WiFi signal distribution is nonstationary, accuracy is insufficient. Therefore, the performance of indoor positioning systems can be enhanced using multiple signal types. However, the positioning performance of each signal type varies depending on the characteristics of the environment. Considering the variability of the performances of different signal types, an F-score-weighted indoor positioning algorithm, which integrates WiFi-RSS and MF fingerprints, is proposed in this study. In the proposed approach, the positioning is first performed by maximum likelihood estimation for both WiFi-RSS and magnetic field signal values to calculate the F-score of each signal type. Then, each signal type is combined using F-score values as a weight to estimate a position. The experiments are performed using a publicly available dataset that contains real-world data. Experimental results reveal that the proposed algorithm is efficient in achieving accurate indoor positioning and consolidates the system performance compared to using a single type of signal.