Micro-to nano-scale characterization of the microstructures in the white etching layer (WEL), observed in a Dutch R260 Mn grade rail steel, was performed via various techniques. Retained austenite in the WEL was identified via electron backscatter diffraction (EBSD), automatic crystallographic orientation mapping in transmission electron microscopy (ACOM-TEM), and X-ray diffraction (XRD). EBSD and ACOM-TEM methods were used to quantify grains (size range: 50 nm–4 µm) in the WEL. Transmission electron microscopy (TEM) was used to identify complex heterogeneous microstructural morphologies in the WEL: Nano-twinning substructure with high dislocation density in the WEL close to the rail surface and untransformed cementite and dislocations in the WEL close to the pearlite matrix. Furthermore, atom probe tomography (APT) revealed a heterogeneous through-thickness distribution of alloying elements in the WEL. Accordingly, the WEL is considered a multi-layered martensitic microstructure. These findings are supported by the temperature calculations from the shape analysis of the manganese profile from APT measurements, related to manganese diffusion. The deformation characteristics of the WEL and the pearlite beneath the WEL are discussed based on the EBSD measurements. The role of deformation in the martensitic phase transformation for WEL formation is discussed.