The main purpose of this paper is to manage the container property effectively at the container yard by applying the RTLS technology to the field of port logistics. Yet, many kinds of noises happen to be inputted with the distance value(between the reader and the tag) which is to be inputted into the location identification algorithm, which makes the distance value jumped due to the system noise of the ultrasonic sensor module and the measurement noise. The Kalman Filter is widely used to prevent this jump occurrence; the noises are eliminated by using the EKF(Extended Kalman Filter) while considering that the distance information of the ultrasonic sensor is non-linear. Also, the 3D RTLS system at the port container yard suggested in this research is designed not to be interrupted for its ultrasonic transmission by positioning the antenna at the front of each sector of the container where the active tags are installed. We positioned the readers, which function as antennas for location identification, to four places randomly in the absolute coordinate and let the positions of the active tags identified by using the distance data delivered from the active tags. For the location identification algorithm used in this paper, the triangulation measurement that is most used in general is applied and newly reorganized to calculate the position of the container. In the first experiment, we dealt with the error resulting in the angle and the distance of the ultrasonic sensor module, which is the most important in the hardware performance; in the second, we evaluated the performance of the location identification algorithm, which is the most important in the software performance, and tested the noise cancellation effects for the EKF. According to the experiment result, the ultrasonic sensor showed an average of 3 to 5cm error up to $45^{circ}$ in case of $60^{circ}$ or more, non-reliable linear distances were obtained. In addition, the evaluation of the algorithm performance showed an average of $4^{circ}{sim}5^{circ}$ error due to the error of the linear distance-this error is negligible for most container location identifications. Lastly, the experiment results of noise cancellation and jump preservation by using the EKF showed that noises were removed in the distance information which was entered from the input of the ultrasonic sensor and as a result, only signal was extracted; thus, jumps were able to be removed and the exact distance information between the ultrasonic sensors could be obtained.