Masters made his Brentford debut against Blackpool in the first game of the 2006-2007 season stepping in for Stuart Nelson who was suspended. Masters spent a period on loan at Slough Town in the 2005-6 season. On October 23, 2006 various newspapers linked Clark Masters with a move to Premiership giants Arsenal and Brentford assistant manager John Griffin was hailing him as a future England goalkeeper.
On 12 March2007 Masters appeared at HastingsMagistrates' Court and pleaded guilty to exceeding the speed limit on De La Warr Road, Bexhill on 2 June2006. Showing complete remorse for his transgression the Magistrates' Court sentenced him to pay a fine of £150, disqualified him from driving for 42 days and ordered that he pay costs of £100.
On March 16, 2007, Masters joined AFC Wimbledon in a one-month loan deal. He played five games for the Dons, including two clean sheets, before being recalled by Brentford. He embarked on another loan spell, this time with Welling United, on August 31, 2007.