Vortex-induced vibration (VIV) of flexible cylinders is an important phenomenon in ocean structures, which may cause fatigue damage and structural failure of offshore structures. Much literature has extensively explored VIV of flexible cylinders under various flow conditions, such as uniform and linearly varying shear flow. However, real scenarios in most cases involve non-uniform, non-linearly varying shear flow profiles. Hence, it is important to investigate the VIV response of the flexible cylindrical structures subjected to non-linearly varying shear flow profiles. This study employs a wake oscillator model (WOM) that simulates the VIV response of the flexible cylinder under the action of non-linearly varying shear flow velocity profiles. The flexible cylinder subjected to linearly varying sheared flow velocity profiles not only overpredicts but also underpredicts the VIV responses compared to the non-linearly varying sheared flow profile, which represents the real scenario. The VIV mode number for the flexible cylinder subjected to non-linear shear flow was found to have a non-linear relationship with that of linear shear flow. The VIV response of the flexible cylinder subjected to a linearly varying shear flow profile exhibits more travelling wave behaviour compared to non-linear shear flow. The location of the maximum VIV response of the structure having the same aspect ratio (L/D) and shear parameter (β), was different for linear and non-linear flow profiles across the span. The time and frequency domain responses showed a shift in the frequency band. The results obtained from the numerical simulations give better insights into the vibrational behaviour of flexible cylinders in realistic flow environments.