During retinal surgical treatment often the gel-like vitreous humor is replaced by aqueous substitutes. A two-dimensional computational model is developed for simulating transpupillary thermotherapy (TTT) process in a human eye under post-retinal treatment. The model accounts for natural convection in vitreous humor and the choroidal blood perfusion. Time dependent and steady state forms of Pennes bio heat transfer and the natural convection governing energy equations are solved using finite volume formulation. The results for steady state and at the end of 60 s of the laser irradiated TTT process show that flow in vitreous humor is significant. The velocity contours indicate strong natural convection on the upper half of the vitreous chamber. Compared with the stationary vitreous case, the peak temperature in retina during TTT, drops by 15 K and 12.5 K due to natural convection flow in the vitreous humor under steady and transient states, respectively. The choroidal blood perfusion also reduces the peak retinal temperature by 6 K and 1.5 K in steady state and transient cases, respectively. The vitreous humor convection enhances heat transfer in the regions adjacent to the laser spot. The temperature rise and the associated thermal damage in the neighboring regions resulting from the flow of vitreous humor is presented. Copyright © 2013 John Wiley & Sons, Ltd.