A system for controlling fan operation of an agricultural implement includes a tank configured to store an agricultural product and a conduit configured to receive the dispensed agricultural product. Furthermore, the implement includes a conduit fan configured to supply pressurized air to the conduit such that the pressurized air conveys the dispensed agricultural product through the conduit and a tank fan configured to supply pressurized air to the tank. Additionally, a computing system is configured to determine a first pressure of the pressurized air within the conduit and a second pressure of the pressurized air within the tank based. Moreover, the computing system is configured to determine a pressure differential between the first and second pressures. Furthermore, the computing system is configured to control a flow of the pressurized air supplied to the tank based on the determined pressure differential.