A 3D transient thermo-metallurgical finite element simulation of a narrow gap multi-layer gas metal arc welding of the first ten layers of a 60E1 profile and R350HT steel rail was implemented in SYSWELD® to study the evolution of the temperature field, phase fractions, and the hardness in the heat-affected zone. For validation, T (t) curves and metallography samples from corresponding instrumented welding experiments were used. Good agreement was reached for what concerns the results of the simulated temperature field and phase transformations. An inhomogeneous evolution of the temperature field throughout the welded layers as a result of the rail’s geometry and welding sequence could be depicted. Based on the simulation results, preheating is believed necessary in order to fully avoid the formation of undesirable Bainite fractions. The hardness simulation showed good results in sidewise locations with regard to the rail cross section and closer to the line of fusion. However, results were less accurate in the middle of the rail cross section and the more the comparison points approached the so called soft zone at the outer border of the heat affected zone and the base material.