Antarctic sea ice areas have only been the main focus for a few studies combining observations and three‐dimensional atmospheric model experiments. This study presents simulations over the Weddell Sea in early summer, applying the polar‐optimized version of the Weather Research and Forecasting model (Polar WRF). The results are compared against observations from the drifting experiment Ice Station Polarstern, which took place on 28 November 2004–2 January 2005. The Polar WRF model showed good skill in simulating synoptic‐scale variations. The diurnal cycles of surface variables were reproduced, but the amplitude was overestimated for most of the variables and the simulations were characterized by a cold temperature bias at night. The major challenges related to the modelling of the atmosphere over Antarctic sea ice were found to be associated with clouds, atmospheric boundary‐layer processes and processes in the sea ice and snow layer. Temporal variations in the errors in cloud cover generated large errors in long‐wave radiation fluxes. In the boundary layer, the overestimated downward sensible heat flux was partly compensated for by the underestimated downward long‐wave radiation at the surface. The underestimated downward long‐wave flux started to dominate as the stability increased and generated the cold temperature bias at the surface. Problems with the surface energy balance, as found in this study, could be reduced by applying more advanced schemes for snow and ice thermodynamics.