Jim Gavin's appointment as manager of Dublin in October 2012 resulted in Cluxton taking over the captaincy of the team. On 28 April 2013, he won his first silverware as captain when the Dublin team defeated Tyrone by 0–18 to 0–17 to win the National Football League title for the first time in 20 years. He later won a ninth Leinster Championship medal when he captained Dublin to a 2–15 to 0–14 defeat of Meath in the final. He was later criticised on "The Sunday Game" for time wasting by taking 7 minutes and 54 seconds to take seven frees during the game. On 22 September 2013, Cluxton captained Dublin for the first time in an All-Ireland final. He ended the game as Dublin's second top scorer with two points from frees in Dublin's 2–12 to 1–14 defeat of Mayo. Cluxton ended the year by winning a fifth All Star Award, while he was also nominated for Football of the Year for a second time. On 27 April 2014, Cluxton won a second successive National League medal as captain of the team following Dublin's 3–19 to 1–10 defeat of Derry in defending their title. He later won his 10th Leinster Championship medal as Dublin retained the title for a fourth successive year following a 3–20 to 1–10 defeat of Meath. Dublin later surrendered their All-Ireland title, however, Cluxton ended the season with another All Star nomination but lost out to Donegal's Paul Durcan for the second time in three seasons. Cluxton captained Dublin to a third successive National League title on 26 April 2015 after a 1–12 to 2–07 defeat of Cork in the final. Later that season Dublin's dominance continued in the Leinster Championship, with Cluxton winning an 11th provincial medal when he captained Dublin to a 2–13 to 0–06 defeat of Westmeath in the final. On 20 September 2015, he became the first goalkeeper to score in three All-Ireland finals when he captained Dublin to a 0–12 to 0–09 defeat of Kerry. It was his third All-Ireland winners' medal. Cluxton again lead Dublin to an All-Ireland Final in 2016 against Mayo. This ended a draw after a relatively poor game due to difficult weather conditions, on a scoreline of 2–09 to 0–15. He captained Dublin to win the replay on a scoreline of 1–15 to 1–14.