At the start of the 2016 season, Ueda started the season well when he helped Kashima Antlers keep two clean sheets in the first two league matches of the season. Ueda also managed to regained his first team place, playing in the centre–back position. After the match in a 3–0 win against Shonan Bellmare on 16 April 2016, he was in tears in a post-match interview and dedicate the win to his family and people who were in situation at Kumamoto earthquakes. Ueda later helped the side finish first place in the first stage of the league. However, he soon found himself placed on the substitute bench for the rest of the 2016 season. Despite this, Ueda continued to be involved in the Kashima Antlers’ first team and helped the side finish at the top of the table. Although he made one appearance in the Championship stage, the club win the league after playing both legs to beat Urawa Red Diamonds 2–2 on aggregate through away goal. Ueda appeared three out of the four matches in the FIFA Club World Cup, as he helped Kashima Antlers reach the final, only to lose 4–2 against Real Madrid. Despite losing in the final, both Ueda and Gen Shoji's centre-back partnership were praised by the media, both in and outside of Japan. Ueda then featured for the next two matches by beating Sanfrecce Hiroshima and Yokohama F. Marinos to reach the Emperor's Cup Final. He then started in the final, starting the whole game, in a 2–1 win against Kawasaki Frontale. At the end of the 2016 season, Ueda went on to make thirty–one appearances in all competitions.