In the 2008–09 season, Henderson's first team place was shared with loan signing David Martin. He started the first game of the season against Milton Keynes Dons, keeping a clean sheet in a 2–0 victory. On 23 September 2008, he saved two shots from a penalty shoot-out in a Football League Trophy match against Lincoln, with Leicester winning 3–1 on penalties. However, Henderson conceded two goals in the next round in a 2–0 defeat to Rotherham United, a match which manager Nigel Pearson described as their worst performance of the season. After a show of poor form from David Martin, Henderson was given a run in the first team in November 2008, but suffered a groin injury that same month in a 2–1 win at Scunthorpe United, which would turn out to be his last appearance for the club. David Martin suffered an injury himself in February 2009, resulting in the club eventually having to sign three goalkeepers on loan, including David Stockdale and Tony Warner. Nonetheless, he was presented with a medal on 24 April after Leicester had won the League One title.