Maflin won three matches to reach the final round in qualifying for two of the first five ranking events of the 2012/2013 season. These came in the Wuxi Classic where he lost in a deciding frame to Michael Holt, and the International Championship where he lost 2–6 to Mark Davis.&lt;ref name="2012/13"&gt;&lt;/ref&gt; He took advantage of the new flatter qualifying system used in the German Masters, whereby he would only need to win two matches to progress to the main stage in Berlin, by beating Joel Walker and Tom Ford, dropping only a single frame in the process. At the venue Maflin defeated Xiao Guodong 5–4, before losing 3–5 to Holt in the last 16. Maflin had a very good season in the minor-ranking PTC events, with his best results coming at the Gdynia Open and the FFB Open, where was knocked out in the quarter-finals by Jamie Burnett and Rod Lawler respectively. In the latter event Maflin had arguably the best win of his career, by coming back from 0–3 to defeat the in-form Neil Robertson in a televised match. He also reached the last 16 of the Scottish Open (scoring his second maximum break along the way) to help him finish 23rd on the Order of Merit, inside the top 26 who qualified for the Finals. There, Maflin had the best run in a ranking of his career by beating 1997 world champion Ken Doherty 4–2, Lawler and Ben Woollaston both 4–3 to reach the semi-finals. He played Ding Junhui and was outplayed in a 0–4 defeat, only managing to score a total of 52 points in the entire match. Nevertheless, the cheque of £20,000 for reaching the last four was the highest of his career to date. Maflin beat Craig Steadman and Steve Davis to advance to the final round of World Championship Qualifying. He led former world champion Peter Ebdon 8–6 but lost four frames in a row to be denied a place in the World Championship for the first time. He increased his ranking by eight spots during the year to end it world number 64.