He started his career as a youth player at Southend United. He has previously played for Colchester United, Darlington and Bristol City. Colchester United
As a teenager he attracted the attention of England goalkeeping coach Ray Clemence.
He made his first-team debut against Brentford in League One in 2004, as a stand-in for Simon Brown and Richard McKinney.
In the 2004-2005 season, replacing first-choice goalkeeper Aidan Davison, Gerken kept four clean sheets in 17 appearances. More appearances in Colchester"s successful 2005-2006 campaign gave Gerken another four clean sheets, including the crucial 0–0 draw at Yeovil Town that clinched Colchester"s promotion to the Football League Championship.
He signed an extended contract in July 2007, and played 40 League games during the 2007-2008 season, at the end of which Colchester were relegated back to League One. On 15 January 2009, Gerken signed a one-month loan deal with League Two side Darlington.
He went straight into the starting eleven for their next game, a 5–1 defeat of Luton Town.
Bristol City
On 30 June 2009, it was confirmed that Bristol City had completed the signing of Gerken for an undisclosed fee, to end his seven-season stay with Colchester United. Gerken was arrested on suspicion of indecent exposure in the early hours of 25 October 2009 after he was allegedly spotted urinating in public. Gerken made his final game for City on 12 January 2013, in a 4–0 defeat at home to Leicester City.
On 8 May 2013, Gerken was released by Bristol City along with third-choice keeper Lewis Carey.
Ipswich Town
On 12 July 2013 Gerken signed a two-year deal with Ipswich Town. Soon after he joined Ipswich he replaced Scott Loach as the first choice goalkeeper.
He made his debut for Ipswich Town in a 1–1 draw against Birmingham City.