Layer thickness is one of the most important input process parameters in laser powder-bed fusion (LPBF) additive manufacturing (AM) since it directly affects the defects found in the printed products, such as porosity, cracks, and manufacturing rate. In this work, three-dimensional finite element heat transfer model was employed to compare and evaluate two different powder layer thicknesses (20 μm and 40 μm) at varying laser power and scanning speeds. A layer-thickness dependent laser absorptivity approach was considered to improve the prediction accuracy of the proposed model. Single track experiments with stainless steel 17-4PH were conducted to validate the simulation model. Simulation results show good agreement with the experimental results with different layer thicknesses. The corresponding averaged melt pool error for width and depth were 4.2% and 9.1%, respectively. It is found that the melt pool dimensions with different layer thicknesses are similar for the most part with slight variations in the melt pool dimensions using varying laser power and scanning speed. However, the morphology of the melt pool track shows visible changes between different thicknesses.