Taguchi based optimization of natural frequency of perforated stiffened hypars is performed to consider the role of fibre lamination, width/thickness ratio of shell and position of perforation centre along x- and y-direction. Natural frequency of stiffened shell is obtained for simply supported boundary condition using finite element procedure based on L27 orthogonal array (OA) considering three settings of each parameter. Main effect plot is analyzed to identify the significant parameters. Natural frequency becomes maximum for a combination of 450 fibre lamination, width/thickness value of 20 and perforation centre position (0.4, 0.4). Interaction graphs identify the interaction parameters. ANOVA study provides the significant contribution of the parameters considered here. Present analysis identifies width/thickness as the most significant factor and other parameters yield very little significance while no interaction is found to be significant. Width/thickness value of shell yields major (98.64%) contribution to natural frequency and other factors yield very little significance. Residual analysis for natural frequency and confirmatory test validate the present study. S/N ratio gets improved by 38.3% at optimal condition compared to the initial parameter setting.