A 28-day spell as manager of Dunfermline Athletic followed later in 1999, and he later served as assistant manager to Jimmy Calderwood at East End Park. In May 2004, Nicholl followed Calderwood when he took over as manager at Aberdeen,[7] again serving as his assistant until the two parted company with the club in May 2009.[8] He resumed his partnership with Calderwood at Kilmarnock in 2010.