Pennycook campaigned in favour of a "Remain" vote for the 2016 referendum on EU membership and his Greenwich and Woolwich constituency voted 64% to remain. After the referendum results were announced, Pennycook was appointed one of the Shadow Ministers for Brexit in October 2016, and, in accordance with the Labour Party whip, voted for the Bill to trigger Article 50. In September 2019, he resigned as shadow Brexit minister in order to campaign actively in favour of holding a second referendum and unequivocally for the UK to stay in the EU.