In August 2009, Brennan signed for
Spartan South Midlands Football League Premier Division side
Aylesbury. He guided the club to their highest ever finish (fourth in the Southern League Premier Division) to qualify for the playoffs. They reached the final against
Gosport Borough, where they drew 2–2 before losing the game on penalties 5–4. The following season saw promotion to the Conference South, after winning the Southern Premier League by 10 clear points. After a poor start to their first season in the Conference South league, Hemel improved and eventually finished in 9th position, also reaching the First Round of the FA Cup where they lost at Bury 3–1. The 2015–16
National League South season saw Brennan's Hemel narrowly miss out on the playoffs as
Whitehawk pipped them on the final day to fifth place. On 18 September 2018, Brennan and his assistant Stuart Maynard were appointed by team owner
Glenn Tamplin as the managerial team at
National League South side
Billericay Town. However, they both had their contracts terminated by Tamplin after less than four months in the job on Wednesday 16 January 2019. On 12 February 2019, Brennan was named as the new manager of
Isthmian League Premier Division side
Kingstonian. Stuart Maynard was also confirmed as the club's new assistant manager. However, on 16 March 2019, following a breakdown in relations with a club director over player liaison and team strategy, Brennan and Maynard re-evaluated their position and resigned after just five games in charge. On 21 May 2019, Brennan was named as the new manager of
National League South side
Wealdstone, with Stuart Maynard as his assistant manager. In the shortened 2019–20 season, Brennan led the club to automatic promotion to the
National League, as champions of the National League South. In December 2020, he turned down an approach from Barnet F.C. to be their manager. On 2 February 2021, Brennan resigned from his role at Wealdstone, with Maynard remaining at the club.
Barnet On 10 June 2021, Brennan joined National League side
Barnet in the Head of Football role with
Harry Kewell taking on the role of Head Coach. On 20 September 2021, after
Harry Kewell was dismissed as Head Coach from
Barnet F.C. having lost five and drawn two of his seven games, Brennan was appointed as Caretaker Head Coach of the club. On 17 February 2022, Brennan stepped back from his role of Head of Football and became Head Coach on a permanent basis. The
2022–23 season saw Barnet in the play-off picture, ending 2022 in fifth position with Brennan being awarded with the National League Manager of the Month award for December and a new contract until 2026. Brennan was named the National League Manager of the Month for April and Barnet again reached the play-offs during the
2023–24 season after finishing 2nd. Following the conclusion of the season, Barnet stated that Brennan remained fully committed to the club after an approach from
Swindon Town. His loyalty was rewarded as he led the club to the National League title in the
2024–25 season. Following his title success, he was named National League Manager of the Season. In February 2026, Brennan received a nine-game ban from the
Football Association for verbally abusing a female referee during Barnet's home defeat by
Shrewsbury Town on 6 September 2025, during which he was sent off for dissent by referee
Kirsty Dowle. He also received a £2,000 fine and a mandatory education course, but said he did not agree with the FA's decision. ==Managerial statistics==