Cowdenbeath Lennon was appointed as
Cowdenbeath manager on 11 June 2008, replacing
Brian Welsh. Lennon managed the club to two successive promotions amid financial difficulties at the club. In his first season, Lennon led the Blue Brazil to second place in the
2008-09 Scottish Third Division only to lose the promotion play-off final to
Stenhousemuir on penalties. However, as a result of
Livingston's demotion, the club were promoted to the
Scottish Second Division. After their unprecedented promotion to the third tier, Lennon guided the club to the
Scottish First Division for the first time in 16 years with victory over
Brechin City in the play-off final.
St Mirren Lennon was appointed manager of
Scottish Premier League club
St Mirren on 7 June 2010, signing a two-year contract to succeed
Gus MacPherson. Lennon secured the first win of his tenure with a 1–0 win over
Hibernian on 29 August 2010. The Buddies finished the
2010-11 season in 11th place, managing to avoid relegation. Over the summer, Lennon decided to make wholesale changes across the club. Lennon's signings included Scottish internationals,
Gary Teale from
Sheffield Wednesday and
Steven Thompson from
Burnley while replacing long-term assistant manager
Iain Jenkins with
Tommy Craig. St Mirren started the season by beating local rivals
Greenock Morton 4–2 in the
Renfrewshire Cup final and
Aberdeen in the first home game of the
2011-12 season. Lennon agreed a new contract with St Mirren on 23 November 2011, keeping him at the club until the summer of 2014. The following season, Lennon led the Buddies to their first ever
Scottish League Cup triumph in a 3–2
win over
Heart of Midlothian. It was the club's first major silverware since winning the
Scottish Cup in 1987, and the fourth major honour in their history. After the 2013–14 season was completed, St Mirren decided not to offer Lennon a new contract. During his time in Paisley, the club achieved their highest league position in over 20 years, finishing eighth in the
2011-12 and
2013-14 seasons. In October 2017, Lennon was inducted into the club's Hall of Fame, cementing his status as a St Mirren legend.
Scotland Under 21s On 18 February 2015, Lennon was appointed caretaker manager of the
Scotland national under-21 football team. He took charge of one friendly match, a 2–1 victory against Hungary.
Alloa Athletic Lennon was appointed manager of
Alloa Athletic on 7 April 2015, succeeding
Barry Smith on a one-year deal with five matches of the
2014–15 season remaining. Lennon would lead the Wasps to a historic third consecutive season in the
Scottish Championship with victory against
Forfar Athletic in the play-off final. However, after five points from the first 16 games of the
2015-16 season, Lennon resigned on 7 December 2015.
Airdrieonians In March 2016,
Airdrieonians manager
Eddie Wolecki Black suffered a stroke during a
Scottish League One match against
Cowdenbeath. To allow Wolecki Black to recover, on 10 March, Lennon was appointed acting head coach on an interim basis until the end of the
2015–16 season, leading the club to fifth place, a point below the promotion play-offs.
Clyde Lennon returned to management with
Scottish League Two club
Clyde on 13 November 2017, after the departure of
Jim Chapman. The Bully Wee's results improved in the first months of Lennon's tenure, with the club climbing from eighth position to finish the
2017-18 season in fifth place, three points behind the promotion play-offs. On 7 May 2019, Lennon agreed terms to remain as Clyde manager for at least an additional two years, which was later extended to the end of the
2021–22 season. He led the Bully Wee to
Scottish League One on 18 May 2019, after beating
Annan Athletic to win the play-off final, thus ending their nine-year exile in the bottom tier. This saw Lennon receive the
SPFL League Two Manager of the Season award. In their first season back in the third tier, Clyde finished seventh in the
2019-20 season when it was curtailed due to the
COVID-19 pandemic. On 8 April 2022, Lennon put pen to paper on a new two-year contract with the club, on a deal until May 2024. {{cite web|url= https://m.clydefc.co.uk/news/2022/04/08/7091/#.YlCnBmTTUlQ Despite, achieving Clyde’s best start to a league campaign in 11 years during the
2022-23 season, it was confirmed on 31 October, that Lennon had departed the club after a nine-match winless run. The announcement came a week after he was placed on 'paid authorised absence'. {{cite web|url= https://www.clydefc.co.uk/news/2022/10/31/7270/ Having spent five years at the club, Lennon holds the distinction of Clyde's longest-serving manager in over 30 years.
Return to Airdrieonians Lennon returned to Airdrieonians, now in the
Scottish Championship, as successor to
Rhys McCabe on 27 August 2025. {{cite web|url= https://www.airdriefc.com/2526news/250827/danny-lennon-is-new-diamonds-boss ==Managerial statistics==