<p>This article introduces a model to investigate the free vibration behavior of perforated nanobeams with square perforations, supported by a Winkler–Pasternak elastic foundation. The objective is to understand how variations in foundation parameters, filling ratio, and holes affect the vibrational behavior of perforated nanobeams. For the first time, this study systematically investigates the influence of an elastic foundation on the vibrational behavior of perforated nanobeams, offering new insights into their dynamics. The model incorporates small-scale effects via the nonlocal strain gradient theory and employs the Rayleigh–Ritz method to compute frequency parameters under various boundary conditions. The present study’s accuracy is supported by the convergence table and comparison with existing literature in some specific scenarios. Parametric studies highlight the influence of foundation stiffness, filling ratio, and hole number on vibration behavior.</p>