In this paper we present the three-dimensional finite element time domain model of the human eye exposed to pulsed holmium: YAG laser radiation used in thermokeratoplasty procedure. The model is based on the Pennes’ bioheat transfer equation and takes into account the focusing action of the lens. The absorption of laser energy inside the eye tissues is modeled using the Lambert-Beer’s law. Model takes into account the pulse temporal profile. The maximum temperature values obtained from steady state and transient analysis are compared against those reported from other papers. Finally, sensitivity analysis of several parameters on the calculated temperature field is carried out.