This paper investigates the potential for using skirted foundations as an alternative to spudcans in an attempt to mitigate punch-through failure of jack-up rigs during installation and preloading in sand-over-clay deposits. The results from a series of numerical analyses on the skirt length were presented in combination with different conditions of sand-over-clay deposit. Three-dimensional large deformation finite element (LDFE) analyses were carried out using the coupled Eulerian-Lagrangian approach. The sand was represented with a modified Mohr-Coulomb model and the clay with an extended Tresca model. The results showed that the likelihood and severity of punch-through increased with (i) increasing the thickness of the sand layer, (ii) increasing the strength of the clay layer, and (iii) reducing the strength non-homogeneity of the clay layer. The degree of mitigation was increased with increasing the skirt length. An optimal skirt length of 0.25D was suggested accounting for the rig towing constraint. Prediction models have been proposed for assessing (i) the potential for punch-through failure, and (ii) the resistance profile for skirted foundations penetrating sand-over-clay deposits.