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Precise modulation of nozzle flow rates is a critical measure to achieve variable-rate spray applications. An electronic flow rate control system accommodating with microprocessors and pulse width modulation (PWM) controlled solenoid valves was designed to manipulate the output of spray nozzles independently to match tree structures which would be detected with a wide-range laser scanning sensor. The PWM signals to control nozzle flow rates were generated by the microprocessors based on laser sensor detections. Multi-channel driver and protection circuits for activating solenoid valves were developed to modulate variable-rate outputs in real time. An embedded computer PC/104 along with a touch screen was used to process control algorithms and to fulfill communications between the operator and the control system. Laboratory tests demonstrated that the flow rate control system was able to achieve linear nozzle outputs with the duty cycle of PWM-controlled solenoid valves.