On 5 June 2013, Dyer signed for Dundee along with fellow former Morton player Peter MacDonald. Dyer made his debut for the club in the first round of the Scottish Challenge Cup, in a 1–0 win over Alloa Athletic, where he came on for Kevin McBride in the 79th minute. He soon made his league debut in a 0–0 draw against Raith Rovers. After making twenty-four appearances in all competitions, as Dundee won the Scottish Championship and promotion to the Scottish Premiership, Dyer signed a two-year contract extension. He left Dundee at the end of the 2014–15 season, having not been offered a new contract.