Indoor localization is one of the most important topics in wireless navigation systems. The large number of applications that rely on indoor positioning makes advancements in this field important. Fingerprinting is a popular technique that is widely adopted and induces many important localization approaches. Recently, fingerprinting based on mobile robots has received increasing attention. This work focuses on presenting a simple, cost-effective and accurate auto-fingerprinting method for an indoor localization system based on Radio Frequency Identification (RFID) technology and using a two-wheeled robot. With this objective, an assessment of the robot’s navigation is performed in order to investigate its displacement errors and elaborate the required corrections. The latter are integrated in our proposed localization system, which is divided into two stages. From there, the auto-fingerprinting method is implemented while modeling the tag-reader link by the Dual One Slope with Second Order propagation Model (DOSSOM) for environmental calibration, within the offline stage. During the online stage, the robot’s position is estimated by applying DOSSOM followed by multilateration. Experimental localization results show that the proposed method provides a positioning error of 1.22 m at the cumulative distribution function of 90%, while operating with only four RFID active tags and an architecture with reduced complexity.