Placing an inertial measurement unit (IMU) at the 5th lumbar vertebra (L5) is a frequently employed method to assess the whole-body center of mass (CoM) motion during walking. However, such a fixed position approach does not account for instantaneous changes in body segment positions that change the CoM. Therefore, this study aimed to assess the congruence between CoM accelerations obtained from these two methods. The CoM positions were calculated based on trajectory data from 49 markers placed on bony landmarks, and its accelerations were computed using the finite-difference algorithm. Concurrently, accelerations were obtained with an IMU placed at L5, a proxy CoM position. Data were collected from 16 participants. Bland–Altman Limits of Agreement and Statistical Parametric Mapping approaches were used to examine the similarity and differences between accelerations directly obtained from the IMU and those derived from position data of the L5 marker (ML5) and whole-body CoM during a gait cycle. The correlation was moderate between IMU and CoM accelerations (r = 0.58) and was strong between IMU and ML5 or between CoM and ML5 accelerations (r = 0.76). There were significant differences in magnitudes between CoM and ML5 and between CoM and IMU accelerations along the anteroposterior and mediolateral directions during the early loading response, mid-stance, and terminal stance to pre-swing. Such comprehensive understanding of the similarity or discrepancy between CoM accelerations acquired by a single IMU and a camera-based motion capture system could further improve the development of wearable sensor technology for human movement analysis.