At the start of the 2013–14 season, Mackay played all four European matches for St Johnstone. After eliminating Rosenborg, Mackay told BBC Scotland about being proud of going through in the Europa League. Mackay was then one of the players to miss the penalty in the shoot-out when St Johnstone lose on penalty shootout against Minsk after a 1–1 draw on aggregate that led to extra time before it went to penalty shootout. After the match, Mackay was among Minsk's critics after criticising the club's antics. Mackay would then score his first goal of the season, on 17 August 2013, in a 4–0 win over Ross County. Mackay then score his second goal of the season, on 5 October 2013, in a 4–0 win over Inverness CT. Mackay would then score his third goal of the season, on 3 May 2014, in a 2–1 loss against Motherwell. Having played a huge role for the club in reaching the Scottish Cup final, Mackay was captain for the match and played as a right-back, as St Johnstone beat Dundee United 2–0. After the match, Mackay said that winning the Scottish Cup and the medal for the final was worth the wait, having been desperate to lift the trophy. As he lifted the trophy, Mackay recorded himself with GoPro from a unique angle.