Johnston was then appointed as the assistant manager of Odd Down F.C in the 2013–2014 season, with Terry Moore as the club's manager. This was a very successful season, which saw the club finish 4th in the Western League Premier Division, the clubs highest ever finish at the time, and currently the clubs second highest finish. Johnston then took over the reins upon Moore's decision to step down, leading them to 5th in his first season. Johnston then went on to win the Western League Premier Division in only his second year as manager of the club, during the 15/16 season. This was the first and only time that Odd Down have won a division at that level. Despite applying to the FA for promotion to the Southern League, Odd Down failed the ground grading requirements, so runners-up Barnstaple Town were awarded with promotion instead.
