The Scot had been in charge of the young Bees since May 2019 before stepping up to join Keith Andrews’ coaching staff.
Under MacFarlane’s stewardship, Brentford B won the London Senior Cup in 2021/22 and the Premier League Cup in 2022/23.
The team entered the U21 Professional Development League in 2024/25 and won the competition at the first attempt, beating Bournemouth 3-2 in the final at Vitality Stadium.
17 B-team players made their first-team debuts during MacFarlane’s tenure, including Mads Bech, Mads Roerslev and Yehor Yarmoliuk.
MacFarlane was awarded his UEFA Pro Licence in May 2025, which is the highest coaching certification available in Europe.
On the appointment, Andrews said: “Neil has been at the football club for a long time; he understands the club’s values and culture.
“The collaboration and alignment with the B team is something I really want to push and hopefully bring to new levels.
“Neil is a greatly experienced coach and will make a seamless transition to this role.”
