[8] He did not remain long at St Mirren, signing for Aberdeen for £100,000 to act as player-assistant manager to Willie Miller.

[10][11] At the time, Aberdeen were struggling to avoid relegation, and Aitken made a bright start by winning 2–0 against Rangers in his first game as manager,[11] but then lost to part-time Stenhousemuir in the Scottish Cup by the same scoreline.

[11][13][14] The following season saw Aitken invest heavily in the transfer market; signing striker Dean Windass for £750,000 and midfielder Paul Bernard for a club record £1 million.

[11] Bernard struggled to justify his expensive transfer fee[15] whilst Windass' time at Pittodrie was hampered by his on-field indiscipline.

[16] Nevertheless, Aitken led Aberdeen to silverware when they won the Scottish League Cup on 26 November 1995, beating Dundee 2–0 in the final.

[23] On 28 November 2007, he followed McLeish, newly appointed as manager of Birmingham City, to the club as first-team coach alongside Andy Watson.