Surface electromyography (sEMG) is a common technique used in the assessment of local muscle fatigue. As opposed to static contraction situations, sEMG recordings during dynamic contractions are particularly characterised by non-stationary (and non-linear) features. Standard signal processing methods using Fourier and wavelet based procedures demonstrate well known restrictions on time-frequency resolution and the ability to process non-stationary and/or non-linear time-series, thus aggravating the spectral parameters estimation. The Hilbert-Huang transform (HHT), comprising of the empirical mode decomposition (EMD) and Hilbert spectral analysis (HSA), provides a new approach to overcome these issues. The time-dependent median frequency estimate is used as muscle fatigue indicator, and linear regression parameters are derived as fatigue quantifiers. The HHT method is utilised for the analysis of the sEMG signals recorded over quadriceps muscles during cyclic dynamic contractions. The results are compared with those obtained by the Fourier and wavelet based methods. It is shown that HHT procedure provides the most consistent and reliable assessment of spectral and derived linear regression parameters, given the time epoch width and sampling interval in the time domain. The suggested procedure successfully deals with non-stationary and non-linear properties of biomedical signals.