One of the problems in inverse dynamics calculation for the inertial measurement unit (IMU)-based joint force and torque estimation is the amplified signal noises of segment kinematic data mainly due to the differentiation procedure and segmental soft tissue artifacts. In order to deal with this problem, appropriate filtering methods are often recommended for signal enhancement. Conventionally, a low-pass filter (LPF) is widely used for the kinematic data. However, the zero-phase LPF requires post-processing, while the real-time LPF causes an unignorable time lag. For this reason, it is inappropriate to use the LPF for real-time joint torque estimation. This paper proposes a Kalman filter (KF) for inverse dynamics of IMUbased joint torque estimation in real time without any time lag, while utilizing the smoothing capability of the KF. Experimental results showed that the proposed KF outperformed a real-time LPF in the estimation accuracy of hip joint force and torque during jogging on the spot by 100 and 29%, respectively. Although the proposed KF requires the process of adjusting covariance according to the dynamic conditions, it can be expected to improve the estimation performance in the field where joint force and torque need to be estimated in real time.