The linear instability of Faraday waves in Hele–Shaw cells is investigated with consideration of the viscosity of fluids after gap-averaging the governing equations due to the damping from two lateral walls and the dynamic behavior of contact angle. A new hydrodynamic model is thus derived and solved semi-analytically. The contribution of viscosity to critical acceleration amplitude is slight compared to other factors associated with dissipation, and the potential flow theory is sufficient to describe onset based on the present study, but the rotational component of velocity can change the timing of onset largely, which paradoxically comes from the viscosity. The model degenerates into a novel damped Mathieu equation if the viscosity is dropped with two damping terms referring to the gap-averaged damping and dissipation from dynamic contact angle, respectively. The former increases when the gap size decreases, and the latter grows as frequency rises. When it comes to the dispersion relation of Faraday waves, an unusual detuning emerges due to the imaginary part of the gap-averaged damping.