Nicholl had great success as manager of
Raith Rovers, winning the
1994–95 Scottish League Cup and the
1994–95 Scottish First Division championship. Due to their League Cup triumph, Raith qualified for the
1995–96 UEFA Cup and reached the second round, where they were eliminated by eventual winners
Bayern Munich. Raith took a 1–0 lead at the
Olympiastadion thanks to a goal by
Danny Lennon. Bayern recovered to win 2–1 on the night and 4–1 on aggregate. again serving as his assistant until the two parted company with the club in May 2009. He resumed his partnership with Calderwood at
Kilmarnock in 2010. Nicholl was appointed manager of
Cowdenbeath in June 2010, but he left Cowdenbeath at the end of the 2010–11 season after they were relegated from the First Division. Nicholl was then appointed assistant manager of
Kilmarnock for a second time, by
Kenny Shiels on 15 June 2011. Kilmarnock won the
2011–12 Scottish League Cup under Shiels and Nicholl, but Shiels was sacked by Kilmarnock in June 2013. Nicholl then decided to accept the offer of assistant manager at
Hibernian. After manager
Pat Fenlon resigned on 1 November, Nicholl was appointed caretaker manager. Nicholl left Hibernian soon after their new management team was recruited. After leaving Hibernian, Nicholl returned to
Cowdenbeath for a second stint as their manager. He led the Blue Brazil to avoid relegation via the
Scottish Championship play-offs in the
2013–14 season beating local rivals
Dunfermline Athletic in the two-legged final. He led the side to the
Fife Cup that season. However a very difficult season followed in
2014–15, which included a joint-record 10–0 defeat to eventual champions
Heart of Midlothian. The following week, Cowdenbeath managed to draw 0–0 with
Rangers. The club was relegated to
League One on the last day, after which Nicholl resigned as manager. While still at Cowdenbeath, Nicholl had also become assistant manager to
Michael O'Neill with the Northern Ireland national team in March 2015. He was appointed as assistant to new
Falkirk manager
Paul Hartley in October 2017, while also continuing in his role with Northern Ireland. He became assistant manager at
Rangers in January 2018, assisting
Graeme Murty. After Murty left Rangers on 1 May, Nicholl and
Jonatan Johansson were placed in interim charge until the appointment of
Steven Gerrard on 1 June. Nicholl joined
St Mirren as their first team coach in November 2018. He then moved to
Dundee in May 2019, assisting
James McPake. Nicholl was released from the club in June 2020. On 28 June 2020, Nicholl became assistant manager of
Northern Ireland national football team. ==Honours==