A reliable method for deconvolving badly convoluted molecular beam time‐of‐flight waveforms using Fourier transform and Wiener filtering techniques is presented. The devised method places no restrictions on the functional form of any factors affecting the shape of the measured time‐of‐flight distribution, but rather uses an accurately determined distribution to estimate an overall response function for the system. The estimated response function may then be used to deconvolve any convoluted time‐of‐flight waveform measured under similar experimental conditions. The mathematical details of the method are discussed and examples of its application to the deconvolution of time‐of‐flight waveforms measured in unchopped pulsed supersonic beams of argon, krypton, CHCl3, and CH3Cl are presented.