On 13 January 2017, after a frustrating first half of the campaign with RB Leipzig and due to their acquisition of defender Dayot Upamecano from Salzburg during the winter transfer window, Papadopoulos moved to Hamburger SV. The HSV manager Markus Gisdol knew the defender from their time together at Schalke 04. On 21 January 2017, he made his debut with the club as a starter in a 1–0 away loss to VfL Wolfsburg. On 3 February 2017 Papadopoulos scored a headed goal from a set piece against Bayer Leverkusen, giving Hamburg a 1–0 victory over his parent club. A week later, HSV celebrated back-to-back Bundesliga wins for only the second time this season as Papadopoulos scored against his last club in a 3–0 away win at RB Leipzig.