At the end of the 2010/2011 season, with 12 months left on his contract, Kováč left for 2011 Swiss Super League champions F.C. Basel for an undisclosed fee on a two year contract.
At the end of the 2010/2011 season, with twelve months left on his contract and after 62 league and cup appearances, Kováč left West Ham United. In July 2011 Kováč joined 2011 Swiss Super League champions F.C. Basel for an undisclosed fee on a two-year contract.