Dundee United
On 1 July 2003, Kerr moved to Dundee United on a Bosman transfer, signing a three–year contract. Their manager Ian McCall had been keeping tabs on the Scotland Under-21 player since he himself left Falkirk.
Kerr made his debut for the club, starting the whole game, in a 2–1 loss against Hibernian in the opening game of the season. He soon settled at Tannadice and became a regular in the side. Between mid–October and November, he appeared once for Dundee United, due to being on the substitute bench. On 29 February 2004, Kerr scored his first goal for the Tangerines, in a 2–0 win against Rangers. By the end of his first season, he had racked up 33 League and two cup appearances and scoring once in all competitions. His tenacity in midfield was a feature of the latter part of the campaign in which United finished strongly to take fifth place, their best finish since 1996–97 season.
Commencing the 2004–05 season in the starting eleven, Kerr scored his first goal of the season, in a 3–1 win against Stranraer in the second round of the Scottish League Cup at Tannadice. However, he suffered a dip in form and only appeared another four times before making his way back into the first team at the turn of the year. Kerr then scored his second goal of the season, in a 4–3 thrilling win against Gretna in the third round of the Scottish Cup. He went on to miss only one more match throughout the rest of the season, and became a vital part of the midfield as Gordon Chisholm became manager. Following the 1–1 draw against Inverness Caledonian Thistle on 19 February 2005, Kerr was subjected of abuse by Dundee United's supporters. Despite this, he came on as a 66th-minute substitute, and helped the Tangerines beat Hibernian 2–1 to reach the final. In the derby match against Dundee on 30 April 2005, Kerr produced a Man of the Match performance, in a 2–1 win. In the last game of the season against Inverness Caledonian Thistle, he helped Dundee United win 1–0 to secure the Scottish Premier League status. Kerr played the entirety of the final, as the match ended with the Tangerines loss 1–0 to Celtic. At the end of the 2004–05 season, he went on to make thirty–seven appearances and scoring two times in all competitions.
At the start of the 2005–06 season, Kerr made his European debut, starting the whole game, in a 0–0 draw against MyPa in the first leg of the UEFA Cup second qualifying round. On 19 August 2005, he signed a three–year contract with Dundee United, keeping him until 2008. In the return leg, Kerr scored his first European goal, in a 2–2 draw, as the Tangerines were eliminated from the tournament on away goal. He continued to regain his first team place in the midfield position. His performances was praised by manager Gordon Chisholm, saying: "he has started the season very well and I think his critics have finally been won over." On 11 March 2006, Kerr scored his first league goal of the season, in a 3–1 win against Livingston. At the end of the 2005–06 season, Kerr made thirty–eight appearances and scoring two times in all competitions.
At the start of the 2006–07 season, Kerr set up two goals for Dundee United in two separate matches, coming against Rangers and St Mirren. Since the start of the 2006–07 season, he continued to regain his first team place in the midfield position. During a match against Inverness Caledonian Thistle on 16 September 2006, Kerr was ill and was substituted in the 53rd minute, as the Tangerines drew 0–0. Shortly after, manager Craig Brewster revealed that he returned to training the next day despite his illness, saying: "Mark was ill during the Inverness game so we took him off but he's back in again now and has been training as hard as usual. His attitude is first-class and he's a great professional." When Dundee United meet Inverness Caledonian Thistle again in the fourth round of Scottish Cup on 3 February 2007, Kerr earned a Man of the Match award for his performance despite losing 1–0. After missing two matches through suspension (up until his suspension, he appeared in every match for the Tangerines), Kerr returned to the starting line–up, starting the whole game, in a 2–0 loss against St Mirren on 5 May 2007. At the end of the 2006–07 season, he made forty appearances in all competitions.
At the start of the 2007–08 season, Kerr suffered an injury that saw him not play in the first two league matches. He made his first appearance of the season, in a 0–0 draw against Hibernian on 18 August 2007. Following his return from injury, Kerr found his playing time, coming from the substitute bench. On 10 November 2007, he made his first league starts in three months, and gave his excellent performance, in a 2–0 win against Kilmarnock. Following this, Kerr won back his first team place in the starting eleven. In the 2008 Scottish League Cup Final, with his team 1–0 ahead in the closing minutes of normal time, he was responsible for a careless backpass pounced upon by Kris Boyd who equalised for Rangers; the game moved into extra time and a penalty shoot-out, which United lost. After the match, Kerr apologised to the team for letting them down. Despite this, he remained in the first team for the remainder of the season. At the end of the 2007–08 season, Kerr made thirty–eight appearances in all competitions. Kerr chose to leave when his contract expired at the end of June 2008.
