The present disclosure provides a new and innovative method and system for flow rate compensation in devices, such as medical devices and other electronic devices. In various embodiments, a computer-implemented method includes dispensing, by a pump controlled by a controller, a fluid from a fluid supply in a pulse mode over a period by determining a pulse volume for a pulse, determining a pulse cycle time, and for the period: controlling the position of the pump to perform a delay and perform a pulse to dispense an amount of the fluid, the pulse performed for the pulse cycle time, calculating an overshoot or undershoot of the amount of the fluid dispensed relative to the pulse volume, adjusting the pulse cycle time based on the calculated overshoot or undershoot, and repeating the dispensing until the period has elapsed.