Doherty began the 2012–13 season by losing 4–5 to Stuart Bingham in the second round of the Wuxi Classic and 3–5 to Martin Gould in the first round of the Australian Goldfields Open.&lt;ref name="2012/13"&gt;&lt;/ref&gt; He finally compiled the first official 147 break of his career at the minor-ranking 2012 Paul Hunter Classic in Germany during a first round win against Julian Treiber. He went on to reach the quarter-finals of the event, losing 0–4 to Mark Selby. Doherty was defeated in qualifying for the Shanghai Masters and the 2012 UK Championship and failed to advance beyond the wildcard round of the International Championship. At the fifth European Tour Event, the Scottish Open, he saw off the likes of Luca Brecel and Ryan Day to reach the semi-finals where he lost 2–4 against Ding Junhui. Doherty was eliminated in the first round of the German Masters by Peter Lines, but then had his best run of the season at the Welsh Open. He beat four-time world champion John Higgins 4–1 and Tom Ford 4–3 to make it through to the quarter-finals. He led Stuart Bingham 2–0, but a series of missed pots saw Doherty lose his confidence and he went on to lose 3–5. His aforementioned run to the semi-finals of the Scottish Open helped him finish 16th on the PTC Order of Merit to qualify as one of the top 26 players for the Finals, but he lost 2–4 to Kurt Maflin in the first round. Doherty almost pulled off one of his trademark comebacks against Matthew Selt in the final round of World Championship qualifying as from 4–9 down he levelled at 9–9, but lost the deciding frame. The result meant that this was the first season where Doherty had not featured in any of snooker's Triple Crown events. Doherty increased his ranking by eight spots during the season to finish it ranked world number 27.