A 3D numerical model is developed which can simulate the melting of phase change material (PCM) with natural convection inside a PCM capsule subjected to the flow of heat transfer fluid (HTF) outside the capsule. The model captures the combined effect of HTF flow and natural convection which governs the melting pattern inside the capsule. The model consists of a heat transfer and phase change model, and a fluid flow model. The governing equations are discretized using finite volume method and implemented by developing an in-house program in Fortran. Results show that the melting rate is increased with the decrease in capsule size, increase in HTF inlet temperature and velocity, and for inlet from the bottom. Also, the effect of natural convection is enhanced for larger capsules, higher HTF inlet temperature and velocity, and HTF flow inlet from the bottom of the domain. Results show that there is 27.04% decrease in melting time for a 6 mm radius capsule if natural convection is considered. It is also seen that the melting time is reduced by 15.04% and 13.88% due to natural convection for flow from bottom and from top, respectively.