The regularities and formation mechanisms of structural-phase states and properties at different depths in the rail heads along the central axis and fillet after differential quenching of 100-meter rails and extremely long operation (with passed tonnage of 1411 million tons gross weight) have been revealed by the methods of the state-of-the-art physical materials science. As revealed, the differential quenching is accompanied by the formation of morphologically multi-aspect structure presented by grains of lamellar perlite, ferrite–carbide mixture, and structure-free ferrite. The steel structure is characterized by the α-Fe lattice parameter, the level of microstresses, the size of coherent-scattering region, the value of interlamellar distance, the scalar and excess dislocation densities. As shown, the extremely long operation of rails is accompanied by the numerous transformations of metal structure of rail head: firstly, a fracture of lamellar pearlite structure and a formation of subgrain structure of submicron (100–150 nm) sizes in the bulk of pearlite colonies; secondly, a precipitation of carbide phase particles of nanometer range along the boundaries and in the bulk of subgrains; thirdly, a microdistortion growth of steel crystal lattice; fourthly, a strain hardening of metal resulting in the increase (by 1.5-fold) in scalar and excess dislocation densities relative to the initial state. A long-term operation of rails is accompanied by the formation of structural constituent gradient consisting in a regular change in the relative content of lamellar pearlite, fractured pearlite, and structure of ferrite–carbide mixture along cross-section of railhead. As the distance to the rail fillet surface decreases, a relative content of metal volume with lamellar pearlite decreases, and that with the structure of fractured pearlite and ferrite–carbide mixture increases. As determined, the characteristic feature of ferrite–carbide mixture structure is a nanosize range of grains, subgrains and carbide-phase particles forming it. The size of grains and subgrains forming the type of structure varies in the limits of 40–70 nm; the size of carbide-phase particles located along the boundaries of grains and subgrains varies in the limits of 8–20 nm. A multiaspect character of steel strengthening is detected that is caused by several factors: firstly, the substructural strengthening due to the formation of fragment subboundaries, whose boundaries are stabilized by the carbide-phase particles; secondly, the strengthening by carbide-phase particles located in the bulk of fragments and on elements of dislocation substructure (dispersion hardening); thirdly, the strengthening caused by the precipitation of carbon atoms on dislocations (formation of Cottrell atmospheres); fourthly, the strengthening being introduced by internal stress fields due to incompatibility of crystal-lattices’ deformation of α-phase structural constituents and carbide-phase particles.