In February 2011, Faber was appointed as assistant manager of Bert van Marwijk at the Netherlands national team. After Faber accepted the national team job, his performances with FC Eindhoven went downhill. With four points from the following eleven matches, FC Eindhoven missed out on a play-off spot. In the 2011–12 season, the FC Eindhoven performances were again above expectations. The team were third in the Eerste Divisie at the time Faber left the club. In March 2012, Faber returned to PSV as assistant manager after Fred Rutten was sacked as manager. Phillip Cocu was chosen as caretaker. Unlike Cocu, Faber's role was permanent after agreeing on a two-and-a-half-year contract. Faber was present at UEFA Euro 2012 when the Dutch team were knocked out in the group stage. After Van Marwijk resigned in the wake of the elimination, Faber also quit to fully focus on his job at PSV. Despite receiving several managing position offers in 2013, Faber signed a new two-year contract and continued to work as assistant manager after the appointment of Cocu as PSV manager.