Finite-difference numerical solutions were obtained to present the flow and temperature field details within the transient Ekman layer during spin-up of a thermally stratified fluid in a cylinder. This complements the earlier studies on stratified spin-up which examined the flows in the interior core region. As the stratification increases, the following changes in the flow field are noticeable. The radial velocity in the Ekman layer decreases in magnitude. The azimuthal flows adjust smoothly from the interior region to the endwall boundary, and the Ekman layer in the azimuthal flow field fades. Vertical motions are inhibited, resulting in a weakened Ekman pumping. The axial vorticity field behaves similarly to the azimuthal flows. The temperature deviation from the equilibrium profile decreases, and the heat transfer flux from the endwall to the fluid decreases. The thickness of the thermal layer is larger than the velocity layer thickness. Illustrative comparisons of the relative sizes of the terms in the governing equations are conducted in order to assess the stratification effect in the adjustment process of the fluid.