He decided to move back to KR Reykjavík in 2007 to finish off his career. He took over as head coach at KR halfway through the 2010 season and managed the team for four seasons. During that time, KR Reykjavík won two league titles (2011 and 2013) and three cup titles (2011, 2012 and 2014). Rúnar left KR November 2014, to manage his former club Lillestrøm SK.