With the increase in electricity consumption and price, energy efficiency in industrial refrigeration systems becomes an even more important issue. The performance of the industrial refrigeration system can be reported by creating energy labeling according to the energy efficiency index value. In this study, the industrial refrigeration system was evaluated in terms of energy performance with proposed a fan control technique and performed an environmentally friendly design using propane (R290) refrigerant. In addition, a new control process was developed for the management of evaporator and condenser fans, and the effect of this process on the cooled package temperatures and energy consumption was investigated. With this new technique, a 25.2% improvement was achieved in the total energy consumption of the industrial refrigeration system. It was observed that the cooled package temperatures were between −1 and +5°C throughout the experiment. The EEI value of the industrial refrigeration system has increased from class “E” to class “D” using a new control technique.