A flame sensing system having a flame rod, a signal generator, a signal measurement circuit, and a controller, where the frequency and/or amplitude of the excitation signal may be variable. The signal measurement circuit may include a bias circuitry that references the flame signal to a voltage, a capacitor that varies the filtration, an AC coupling capacitor, a current limiting resistor, and a low-pass filter. The system may determine the flame-sensing rod contamination, the stray capacitance of the flame sensing system, and compensate for stray capacitance in the flame sensing system. The flame model may include a circuit that simulates a flame in the presence of the sensing rod, and another circuit that simulates a contact surface between the flame and the sensing rod.