On 11 July 2012, Lynch signed a 3-year deal with Huddersfield Town after turning down a new deal at former club Forest becoming manager Simon Grayson's fifth signing of 2012–13 season. Lynch was given the number 33 shirt for the 2012–13 season by manager Simon Grayson on 14 July 2012. He made his league début in the 1–0 defeat by Cardiff City at the Cardiff City Stadium on 17 August. On 25 August he scored his first goal in a league match against Burnley when he gave Huddersfield a 1–0 lead, where Huddersfield won 2–0 in the end. Lynch received his first red card of his Huddersfield career at Hillsborough Stadium in Huddersfield's 3–1 win over Sheffield Wednesday.