The temperature rise inside VRFB stack may exceed its safe limit at higher charging and discharging currents leading to thermal precipitation. A thermal management and control model of VRFB is developed in this paper for the first time in MATLAB/Simulink environment and experimentally validated in the lab. Online monitoring of VRFB stack temperature and flow rate control is executed by dsPIC microcontroller platform. The usual practice of applying higher flow rate by increasing pump speed during charging and discharging operations for keeping the stack temperature within safe limit leads to reduction of overall VRFB system efficiency due to higher pump power loss. In this work a model for determining the dynamic optimal flow rate is developed to ensure efficient thermal management and improvement of overall system efficiency of VRFB. The proposed thermal management scheme is validated by a practical 1 kW 6 h VRFB system operation. It is observed that at a lower flow rate of 180 ml/sec the stack temperature during fast charging and discharging at the rate of 60A rises up to 47 degrees C which is well above the specified safe limit of operating temperature of VRFB and leads to incomplete charging due to premature thermal shut down of the system. Increasing the flow rate to 300 ml/sec keeps the stack temperature within safe limit but the overall VRFB efficiency becomes around 83%. However, by applying dynamic optimal flow rate (160-300 ml/sec) over the range of SOC (10-90%), this is managed within the safe level of 35.8 degrees C and at the same time improving the overall VRFB system efficiency up to 88.55%. The model performance shows very good agreement with the experimental results having maximum error of 0.85%. The thermal management and control scheme demonstrated in this paper is a generalised one and hence very useful for large scale VRFB applications as well.