This present study depicts the numerical free vibration analysis of laminated composite shells with different size of square cut-outs. By employing the shell 281 element, the numerical data are acquired from the ANSYS APDL. For the present numerical study, validation of the finite element method has been conducted by comparing the present results with those obtained from existing literature. The mesh convergence has also been conducted for all the support conditions considered for present analysis. The various parameters considered for this free vibration study are three boundary conditions (cantilever, simply supported at straight edges curve edges free, clamped at straight edges curve edges free), angle of orientations, i.e., (0/90)2S and (45/−45)2S of shells, position of cut-outs, (eccentric and concentric), and size of concentric and eccentric cut-outs. The natural frequency of laminated composite shells with cut-out is significantly influenced by the aforementioned parameters. This research will also provide essential knowledge and confidence to the designer to effectively design laminated composite perforated shells.