 By 1 September 2011, Frederiksen was released from his employment obligations in the Danske Bank Group, and the following week he was appointed manager of Lyngby, where he was also put in charge of transfers.The same year, he received his UEFA Pro Licence.On 2 May 2013, Esbjerg fB announced that Frederiksen would succeed Jess Thorup as the club's head coach from the start of the 2013–14 Danish Superliga season.