Murphy began the 2012–13 season ranked number six. The first tournament for Murphy was the Wuxi Classic, where he lost in the first round 1–5 against Ken Doherty. Murphy's next tournament was the Six-red World Championship, where he finished first in Group E with four wins out of five matches and advanced to the knock-out stage. There he defeated James Wattana, Barry Hawkins, Dominic Dale and Judd Trump to reach the final, but lost 4–8 against Mark Davis. He then reached the quarter-finals of the Australian Goldfields Open, but lost 4–5 against Peter Ebdon. Murphy went one better in the next two ranking tournaments, as he reached the semi-finals of the Shanghai Masters and the International Championship, but lost 3–6 against John Higgins and 5–9 against Neil Robertson respectively. Murphy than reached the final of the 2012 UK Championship courtesy of two tight victories. The first against teenager Luca Brecel in the quarter-finals, after Brecel twice had the chance to pot the final pink and black to win the match, then against Ali Carter in which Murphy recovered from 4–8 down and 0–32 in points behind in the deciding frame to win 9–8. He was ultimately defeated by good friend Mark Selby 6–10 in the final. He also participated at the Players Tour Championship, with his best result coming at the third English event, where he reached the semi-finals, but lost 0–4 against Marco Fu. He finished number 29 on the Order of Merit, and couldn't qualify to the Finals.