Bywater joined Derby County in August 2006 on an initial emergency loan deal for two weeks and signed a permanent three-year deal two weeks later for a fee of £225,000. Before the 2006–07 season, he wore the number 43 shirt at Derby as a tribute to his mentor and former goalkeeping coach Les Sealey, who died at the age of 43 in 2001, saying, "Les looked after me most of the time. He took me to training every day, coached me and advised me on life. I know he is watching over me and that he wants me to do well, so that was for him." Bywater made 43 league and cup appearances in the 2006–07 season as Derby reached the Championship play-off final, where they beat West Bromwich Albion 1–0 to secure a place in the Premier League.