AbstractWe present a high‐order spectral element method (SEM) using modal (or hierarchical) basis for modeling of some nonlinear second‐order partial differential equations in two‐dimensional spatial space. The discretization is based on the conforming spectral element technique in space and the semi‐implicit or the explicit finite difference formula in time. Unlike the nodal SEM, which is based on the Lagrange polynomials associated with the Gauss–Lobatto–Legendre or Chebyshev quadrature nodes, the Lobatto polynomials are used in this paper as modal basis. Using modal bases due to their orthogonal properties enables us to exactly obtain the elemental matrices provided that the element‐wise mapping has the constant Jacobian. The difficulty of implementation of modal approximations for nonlinear problems is treated in this paper by expanding the nonlinear terms in the weak form of differential equations in terms of the Lobatto polynomials on each element using the fast Fourier transform (FFT). Utilization of the Fourier interpolation on equidistant points in the FFT algorithm and the enough polynomial order of approximation of the nonlinear terms can lead to minimize the aliasing error. Also, this approach leads to finding numerical solution of a nonlinear differential equation through solving a system of linear algebraic equations. Numerical results for some famous nonlinear equations illustrate efficiency, stability and convergence properties of the approximation scheme, which is exponential in space and up to third‐order in time. Copyright © 2014 John Wiley & Sons, Ltd.