In 2010 he was appointed as CSKA Sofia's assistant coach and interpreter for the Romanian head coach – Ioan Andone. Because of that fact he is known as the "Bulgarian Jose Mourinho". Later he joined the coaching staff of Adalbert Zafirov, Pavel Dotchev and Gjore Jovanovski. Since 21 October 2010 he became temporary head coach of CSKA. The team showed nice results under his charge and he got assigned as permanent head coach. His assistants were Todor Yanchev (team's captain) and Svetoslav Petrov. He got in charge of the team, when they were 11th in the league and drove them to 3rd place at the end of the season. In addition, in the same season he managed to win the Bulgarian Cup and Bulgarian Supercup. In late October 2011, Radukanov vacated the position of head coach of CSKA Sofia after mutual consent just before the Eternal derby match.
On 28 October 2011, Bulgarian B PFG side Botev Plovdiv announced on their official website, that they had reached an agreement with Milen Radukanov to take over the manager position at the club. In April 2012, he vacated the position of head coach of Botev Plovdiv following a draw with Etar Veliko Tarnovo. Radukanov was reappointed as CSKA Sofia coach on 11 March 2013, after the club had parted ways with Miodrag Ješić.