In this study, the accuracy and reliability of fully nonlinear method against equivalent linear method for dynamic analysis of soil-structure interaction is investigated comparing the predicted results of both numerical procedures with the results of experimental shaking table tests. An enhanced numerical soil-structure model has been developed which treats the behaviour of the soil and the structure with equal rigour. The soil-structural model comprises a 15 storey structural model resting on a soft soil inside a laminar soil container. The structural model was analysed under three different conditions: (i) fixed base model performing conventional time history dynamic analysis, (ii) flexible base model (considering full soil-structure interaction) conducting equivalent linear dynamic analysis, and (iii) flexible base model performing fully nonlinear dynamic analysis. The results of the above mentioned three cases in terms of lateral storey deflections and inter-storey drifts are determined and compared with the experimental results of shaking table tests. Comparing the experimental results with the numerical analysis predictions, it is noted that equivalent linear method of dynamic analysis underestimates the inelastic seismic response of mid-rise moment resisting building frames resting on soft soils in comparison to the fully nonlinear dynamic analysis method. Thus, inelastic design procedure, using equivalent linear method, cannot adequately guarantee the structural safety for mid-rise building frames resting on soft soils. However, results obtained from the fully nonlinear method of analysis fit the experimental results reasonably well. Therefore, this method is recommended to be used by practicing engineers.