Uneven track settlement inevitably occurs for ballasted track and eventually results in poor track geometry and support stiffness leading to considerably high maintenance cost. Considerable in situ and laboratory experiments have been carried out and empirical formulas have been proposed in order to predict track settlement. Nevertheless, laboratory tests are usually restricted in size for financial reasons and the site characteristics vary significantly to fully understand influential parameters. Therefore, the main aim of the present work is to develop an efficient model capable of replicating localised track settlement for different circumstances. A generic ballasted track simulation package BaTrack is introduced combining the Finite Element (FE) software Abaqus, Python, and Fortran. The three-dimensional (3D) FE model includes rail, sleepers, rail-pads, under sleeper pads (USPs), ballast and foundation layers. An advanced non-linear ballast material model is introduced using porous material properties and extended Drucker-Prager model with hardening and is able to account for different confining pressure values. The model is firstly used for comparison against a series of monotonic triaxial tests and has shown good agreement. It is then validated against a series of full size tests carried out at the Southampton Railway Testing Facility (SRTF). A number of settlement analyses are carried out and characteristics of the stress, contact pressure distribution and void evolution from different track configurations are discussed in detail.