Modern rail construction uses continuous-welded rail (CWR). The presence of very few joints leads to an increasing concern due to the large longitudinal loads caused by restrained thermal expansion and contraction, following seasonal temperature variations. The knowledge of the current state of thermal stress in the rail or, equivalently, the rail neutral temperature (corresponding to zero net longitudinal force) is a key need within the railroad transportation community in order to properly schedule slow-order mandates and prevent derailments. This paper presents a nondestructive diagnostic system for measurement of the neutral temperature in CWR based on nonlinear ultrasonic guided waves. The theoretical part of the study involved the development of a constitutive model in order to explain the origin of nonlinear effects arising in complex waveguides under constrained thermal expansion. A numerical framework has been implemented to predict internal resonance conditions of nonlinear waves in complex waveguides. This theoretical/numerical phase has led to the development of an experimental prototype (Rail-NT) that was tested both in the laboratory and in the field. The results of these experimental tests are also summarized.