Natural materials’ inherently weak nonlinear response demands the design of artificial substitutes to avoid optically large samples and complex phase-matching techniques. Silicon photonic crystals are promising artificial materials for this quest. Their nonlinear properties can be modulated optically, paving the way for applications ranging from ultrafast information processing to quantum technologies. A two-dimensional 15-μm-thick silicon photonic structure, comprising a hexagonal array of air holes traversing the slab’s thickness, has been designed to support a guided resonance for the light with a wavelength of 4-μm. At the resonance conditions, a transverse mode of the light is strongly confined between the holes in the "veins" of the silicon component. Owing to the confinement, the structure exhibits a ratio of nonlinear to linear absorption coefficients threefold higher than the uniform silicon slab of the same thickness. A customised time-resolved Z-scan method with provisions to accommodate ultrafast pump-probe measurements was used to investigate and quantify the non-linear response. We show that optically pumping free charge carriers into the structure decouples the incoming light from the resonance and reduces the non-linear response. The time-resolved measurements suggest that the decoupling is a relatively long-lived effect on the scale comparable to the non-radiative recombination in the bulk material. Moreover, we demonstrate that the excited free carriers are not the source of the nonlinearity, as this property is determined by the structure design.