On 28 January 2012, Agger opened the scoring against Manchester United in the fourth round FA Cup tie, defeating them 2–1. It was his first Liverpool goal since 2010, when he scored in the Europa League tie against Benfica. On 26 February 2012, he helped Liverpool to win their first trophy since 2006 as they won the 2012 Football League Cup Final but injured his ribs during the match. On 7 April 2012, Agger made his return from injury as a second-half substitute against Aston Villa at Anfield, replacing José Enrique and hitting the crossbar with a header late on which led to the equalizer in a 1–1 draw. On 8 May 2012, Agger scored his first Premier League goal of the season in a 4–1 win against Chelsea which was also the last home game of the season for Liverpool.
Agger made his first start of the league campaign in a 3–0 defeat to West Bromwich Albion on 18 August, in which he conceded a penalty and was sent off for a foul on Shane Long. Although the penalty was saved, Liverpool were unable to hold on and slipped to a disappointing defeat. On 5 October, Agger signed a new long term contract with Liverpool. On 12 November, Agger was named 2012 Danish Player of the Year for the second time. On 1 December 2012, Agger scored against Southampton at Anfield, with a 43rd-minute header giving Liverpool a 1–0 win. On 30 December, Agger scored a beautiful header against QPR, assisted by a cross from captain Steven Gerrard. Agger made it 3–0 which also was the final score. Agger reached his 200th appearance for Liverpool on 21 February 2013 in a home Europe League tie against Zenit St. Petersburg. With Liverpool trailing 2–0 from the first leg, the Reds recorded a 3–1 win at Anfield, but were eliminated on away goals.
Agger founded The Agger Foundation in 2012 aiming to help children in need.
Outside of football, Agger is a qualified tattoo artist. He has numerous tattoos including a Viking on his upper right arm, a large drawing of Vikings and a graveyard that spans his whole back, which includes his birth date and the Latin motto "Mors certa, hora incerta" ("death is certain, its hour is uncertain"), forming a memento mori. He also features an intricate band around his left elbow which includes the phrase "Succes er at leve som man selv vil" ("Success is to live as you wish" in Danish). In August 2012, during a period of intense speculation regarding his future at the club, Agger had the letters "YNWA" tattooed on the fingers of his right hand, referencing the anthem of Liverpool F.C., "You'll Never Walk Alone".