A comprehensive robust inversion-based Fourier transformation algorithm has been proposed based on the advantages of Hermite functions for processing even in random-walk data known as the iteratively reweighted least squares fourier transformation (IRLS-FT) method. By using Hermite functions as the basis functions of discretization, the Fourier spectrum was discretized using a series expansion of which the expansion coefficients were given by a solution of a linear inverse problem. The method enabled a quicker determination of the Jacobi matrix as the Hermite functions were considered as the eigenfunctions of the inverse fourier transformation. The process was robustified using the iteratively reweighted least squares (IRLS) method with Steiner weights. The result was a very efficient, robust and resistant procedure with a higher noise reduction capability irrespective of the data acquisition protocols, thus, whether regular or irregular sampling procedure was used in acquiring the data. The Fourier transformation operation was employed in developing the new method because it facilitated data conversion from time to frequency domain. To reduce the noise sensitivity of the IRLS-FT as characterized by the traditional DFT method, the Fourier transformation was formulated as an overdetermined inverse problem permitting the required noise reduction tools to be applied. Traditionally, geophysical data are acquired on a regular equidistant grid, but the continual improvement in survey equipment's and processing tools permits non-equidistant measurements. The new applicability of the IRLS-FT is demonstrated in the reduction to the pole of synthetic magnetic data generated in the regular equidistant array and subsequently randomized to produce non-equidistant measurements along a survey line. In one dimensional study, the IRLS-FT processed waveforms were similar for both equidistant and non-equidistant sampling. An application on magnetic data showed a similar anomaly generation for DFT processed equidistant sampling and IRLS-FT processed non-equidistant sampling, indicating the new method is applicable irrespective of the sampling protocol applied in the field survey or data acquisition process. This data processing abilities of the IRLS-FT method simplifies and fasten field data acquisition as measurements are not necessarily taken on a regular grid, which gives it a competitive advantage over the traditional DFT method.