At the start of the 2018–19 season, Kjær started the whole game in the Supercopa de España against Barcelona, as Sevilla lost 2–1. He regained his first team place, playing in the centre-back position, for the club. This last until a match against SD Huesca on 28 October 2018 when Kjær suffered a hamstring injury in the 24th minute and was substituted as Sevilla won 2–1. Following this, it was announced that he would be sidelined for a month. On 25 November 2018, Kjær returned to the starting line-up against Real Valladolid and kept a clean sheet, in a 1–0 win. He continued to found in and out of the starting line-up despite being plagued by injuries as the 2018–19 season progressed. Despite this, Kjær made 37 appearances in all competitions. Following this, it was expected that he'll be leaving Sevilla ahead of the 2019–20 season.