The effect of applied and residual stresses on the magnetic Barkhausen emission (MBE) profile has been studied in case-carburised En36 steel specimens with 0.65 and 0.95 mm case-depth. The initial MBE profile shows two peaks in lower case-depth specimen and only single peak in higher case-depth specimen. The MBE peaks gradually increase in height with applied tensile stress. Under compression, the first peak in lower case-depth specimen disappears and the dominant second peak decreases in both case-depth specimens. However, after unloading from higher stress levels, the MBE profiles show different behaviour. In lower case-depth specimen, on tensile side, the first peak disappears and the second peak decreases with pre-stress level. On compressive side, the first peak increases while the second peak decreases with pre-stress level. In higher case-depth specimen, on both tensile and compressive sides, the MBE peak decreases with pre-stress, but to different extent. These variations in MBE peaks are correlated with residual stress redistribution in the near-surface and subsurface regions.