Transmission electron microscopy methods were used to analyze the cementite substructure in the head of special-purpose long rails of the DT400IK category, made of hypereutectoid steel, after long-term operation on an experimental track on the Russian Railways ring (the tonnage was 187 million tons). It is noted that the study of various aspects of cementite—its structure, morphology, chemical composition, crystal lattice defects—is relevant. The steel structure is represented by three morphological components at a distance of 10 mm from the sample surface: lamellar perlite, fractured and fragmented perlite. The volume fraction of lamellar perlite in the material is 65%. It is shown that after operation, the cementite plates are bent and separated by ferrite bridges. In the plates of ferrite and cementite, a dislocation substructure is formed, which is of a chaotically distributed and network type in ferrite and of an ordered type in cementite. An increased density of dislocations at the ferrite–cementite interfaces compared to the volume of ferrite plates was noted. Two possible mechanisms of deformation transformation of lamellar perlite grains are indicated: fracture of cementite plates and carbon pulling out from the lattice of the carbide phase. It is indicated that in the dissolution of cementite plates, the interfacial boundaries of “α-phase-cementite” play an important role. The removal of carbon from cementite plates occurs most intensively near defects in ferrite and cementite. The formed nanosized particles of tertiary cementite are unevenly distributed in the ferrite plates; most of them are observed at the locations of ferrite subgrains and interfacial boundaries. This results in non-uniform diffraction contrast in dark-field images of cementite plates. Nanosized particles of cementite can be taken out into the interlamellar space of pearlite colonies in the process of dislocation slip, or they are formed as a result of deformation decomposition, which is less likely. The fragmentation of ferrite and cementite plates is revealed and azimuthal components of total misorientation angles are estimated. The mechanisms of mass transfer of carbon atoms over interstitial sites, deformation vacancies, dislocation tubes, grain boundaries and fragments are considered. According to all the established patterns of the cementite substructure transformation, a comparison with the results for rails made of hypoeutectoid steel was performed.