He returned to the Scottish Championship in January 2017 when he signed a short-term contract with St Mirren. He made 15 appearances for Jack Ross's "Buddies" in the second half of the 2016–17 campaign, including one in the final of the Scottish Challenge Cup at Fir Park, which ended in a 2–1 defeat to Dundee United. In May 2017, Eckersley signed a two-year contract extension, keeping him at St Mirren Park until the summer of 2019. He made 27 appearances across the 2017–18 campaign as the "Saints" secured promotion to the Scottish Premiership as champions of the Championship.