With the increasing integration of intermittent energy sources into the smart grid, distributed battery energy storage systems (DBESSs) are employed to balance power generation and demand. Power allocation among DBESSs plays an important role in maintaining the stability of energy systems. So far, the control of DBESSs has focused on either continuous-time control for continuous-time battery dynamics or discrete-time control for discretized battery dynamics. However, in realistic industrial applications, DBESSs have continuous-time dynamics in nature, and their control is implemented on digital controllers. To tackle this issue, a distributed multirate control system is designed in this article for continuous-time DBESSs. It allocates power by keeping the same relative State-of-Charge (SoC) variation rate for all DBESSs. For the accurate computation of the output/input power without global information, the control strategy consists of distributed multirate estimators each for a DBESS. The operating rate of the estimation algorithm is designed multiple times higher than the sampling rate of the measurement of battery and the sampling rate of the battery controller. With the proposed multirate estimator, a smaller estimation error is achieved. The same relative SoC variation rate and the stability of closed-loop system can be guaranteed. Simulation studies are given to demonstrate the effectiveness of the proposed control strategy.