Experimental studies and numerical modelling of the deformation of soft clay stabilised by stone columns have been conducted over the past few decades. Continuum-based numerical models have provided valuable insight into the prediction of settlement, lateral deformation, and stress and strain-rate dependent behaviour of stone columns at a macroscopic scale, but because they consist of granular material such as crushed rock, gravel, and waste rock aggregates, their behaviour is influenced by inter-particle micromechanics and cannot be modelled properly using these models. In this paper a novel coupled model of the discrete element method (DEM) and finite difference method (FDM) is presented to study the deformation of a single stone column installed in soft ground. In this coupled discrete–continuum method, PFC2D and FLAC were used to model the interaction between the stone column and surrounding clay, respectively. The contact forces at the interface between the two zones were determined through a socket connection that allows the DEM to transfer forces and moments to the FDM and vice versa. The predicted results were comparable to the data measured experimentally, showing that the coupled discrete–continuum model proposed in this study could simulate the load-deformation behaviour of a stone column installed in clay. The contact force distribution and shear stress contour developed in the stone column and surrounding clay were captured to provide a better understanding of the load-deformation behaviour of the stone column.