A fuel injector cleaning system includes an injector cleaning housing that defines a cavity structured to receive a fuel injector. A heater is operatively coupled to the housing. A three-way valve includes a first inlet fluidly coupled to a calibration fluid reservoir, and a second inlet fluidly coupled to a cleaning fluid reservoir. An intake line includes a first end fluidly coupled to an outlet of the valve, and a second end structured to be fluidly coupled to a fuel inlet of the fuel injector. A controller is operatively coupled to each of the heater and the valve. The controller is structured to actuate the valve so as to cause flow of a cleaning fluid to the fuel injector. The heater is operated so as to heat the cleaning fluid. The valve is actuated so as to cause flow of a calibration fluid to the fuel injector.