To study the dynamical behaviour of the engineering and physical systems, we often need to capture their continuous behaviour, which is modeled using differential equations, and perform the frequency-domain analysis of these systems. Traditionally, Fourier transform methods are used to perform this frequency domain analysis using paper-and-pencil based analytical techniques or computer simulations. However, both of these methods are error prone and thus are not suitable for analyzing systems used in safety-critical domains, like medicine and transportation. In order to provide an accurate alternative, we propose to use higher-order-logic theorem proving to conduct the frequency domain analysis of these systems. For this purpose, the paper presents a higher-order-logic formalization of Fourier transform using the HOL-Light theorem prover. In particular, we use the higher-order-logic based formalizations of differential, integral, transcendental and topological theories of multivariable calculus to formally define Fourier transform and reason about the correctness of its classical properties, such as existence, linearity, time shifting, frequency shifting, modulation, time scaling, time reversal and differentiation in time domain, and its relationships with Fourier Cosine, Fourier Sine and Laplace transforms. We use our proposed formalization for the formal verification of the frequency response of a generic n-order linear system, an audio equalizer and a MEMs accelerometer, using the HOL-Light theorem prover.