This paper is the second part of a two-part series which investigates the energy saving potentials in a novel mechanical ventilation system by replacing terminal dampers with decentralized fans. The present study (Part 2) proposes a method to control the main fan as well as the decentralized fans in such a way that the system is balanced for different demand requests. The control method comprises two levels, zone level and system level control, and is based on measuring static pressure in the duct system similar to the energy-efficient control proposed for the conventional ventilation system in Part 1. Two identical experimental mock-ups, one with the dampers and one with the decentralized fans were used in a laboratory environment to evaluate the performance of the novel ventilation system and to compare the two ventilation systems from power use point of view. Experimental results indicate the ability of the proposed method to control the ventilation system with decentralized fans. The measured power use of the two ventilation systems was almost the same for the range of tested total airflow rates, except when the total airflow rate was rather low. Calculations, however, reveal an energy saving potential of around 30% depending on the efficiency of the main fan.