Bopara returned to the England team for the 2013 Champions Trophy, now batting in the number 6 position. He made an unbeaten 46 against Australia to help guide England to victory. In the second game he was again unbeaten, making 33 and also bowled six overs. However, in a close game Sri Lanka won meaning England had to win their last game to qualify. They did so after beating New Zealand, with Bopara taking 2–26 in a low scoring match. England convincingly beat South Africa in the semi final, with Bopara not being required to bat. In the final against India, Bopara took figures of 3–20 and also made 30 during a big partnership with Eoin Morgan, However, once the pair were out the England innings fell apart and India went on to lift the trophy.