3-year contract with Derby on 13 January 2009. He made his 100th appearance for the club away to Blackpool on 8 August 2009, keeping a clean sheet. In December 2009, after keeping two successive clean sheets, manager Nigel Clough praised Bywater's performances in the two games: "Stephen has been exemplary. He is fully fit and approaching the peak of his career. He has a good temperament, which is probably a factor of his age. He works hard in training and, like all goalkeepers, he is a bit daft." An injury sustained away to Reading in March 2010 saw Bywater ruled out for two games which brought to an end a run of 71 consecutive league appearances in the Derby goal. He returned and put in Championship Team of the Week performance as Derby drew 0–0 at Sheffield Wednesday. After Derby secured survival with a 1–1 draw with Crystal Palace, Bywater sat out the last two games of the season to rest a sprained rib joint. He returned to the first team in the 2010–11 season and made his 150th appearance for the club in a 2–0 defeat at Hull City. Bywater played every minute of Derby's opening 11 games of the season, keeping two clean sheets, before a wrist injury sustained in training during the October international break ruled him out for a month. He returned to the first team in November 2011, which coincided with a dreadful run of form which saw Derby drop from 4th to 18th in 3 months. Bywater then sustained an injury in a 1–0 defeat to Hull City on 22 February 2011, ruling him out for several weeks.