On 23 January 2014, Rooney signed a two-and-a-half-year contract with Scottish Premiership side Aberdeen. He scored on his debut two days later in a 2–2 draw with Motherwell at Fir Park, and scored his second in as many matches, as well as crossing for Jonny Hayes’ opening goal, as Aberdeen beat St Johnstone 4–0 to progress to the League Cup Final. Rooney scored his fifth goal in six appearances on 25 February, to help his side end Celtic’s 26-match unbeaten run in the Premiership season. On 8 March 2014, Rooney scored his sixth goal in eight appearances in a 1–0 Scottish Cup quarter-final win over Dumbarton.
Rooney started for Aberdeen against his former club Inverness CT in the 2014 Scottish League Cup Final. A 0–0 scoreline after 90 minutes led to extra time and penalties, where Rooney scored the decisive penalty kick in a 4–2 victory to win the League Cup; it was Aberdeen’s first piece of silverware for 19 years. Rooney was voted SPFL Player of the Month for February 2014.
Rooney started the 2014–2015 season strongly by scoring two goals in a 5–0 home victory against FK Daugava Riga in the first qualifying round of the Europa League. He continued his strong start with a first-half hat-trick in a 3–0 away win in the second leg. Rooney went on to give the Dons the lead in the second leg of the second qualifying round against FC Groningen, scoring a penalty as Aberdeen won 2–1, progressing to the third qualifying round to face Real Sociedad. This put his European goals total with Aberdeen to six in four games. Rooney scored his first league goal of the season in a 3–0 win against Ross County and continued his scoring exploits four days later with his second hat-trick for the Dons and tenth goal of the season in a 4–0 League Cup win against Livingston. Rooney then provided the only goal in a game against Hamilton Academical in the same competition to see the Dons through to the semi-finals. On 23 November, Rooney continued his good form and scored his 14th goal of the season by converting a penalty in a 1–0 victory away against Partick Thistle. On 22 December, Rooney signed a contract extension running until the summer of 2018. Rooney scored 28 goals in total for the season and finished the top scorer in the Scottish Premiership.
On 5 August 2016, Rooney signed a four-year contract extension at Aberdeen. He scored his 100th Scottish League goal on 31 March 2017, in a 7–0 victory over Dundee. On 22 April 2017, in the semi-final of the Scottish Cup, Rooney opened the scoring after just 12 seconds as Aberdeen won 3–2 against Hibernian.