Having only suffered defeat once all season, Boroughmuir travelled to East Lothian with two former Reds stars in their squad.
Neil Rodger (back-row) started the match, while Sam Johnson (scrum-half) was among the replacements.
Meanwhile, Bryan Craig's side were without regular half-back pairing Liam Clutton and Nick Bell, so Jamie Paterson started in the nine jersey with James Ferguson moving to 10.
There were recalls on the wings for Andrew Symington and Kyle Adams, as Euan Herkes returned from injury in the midfield.
Visiting stand-off Graeme Blackhall kicked the first points of the afternoon to put Muir in front early on, and they extended that lead soon after when back-row Will Kay crashed over.
10-0 down after the first quarter, the Reds needed to score next, and they did when stand-off Ferguson broke and found the returning Herkes, who capped his return to the side with a try.
Ferguson converted and the gap was down to just three points.
However, the visitors struck back with two tries of their own before half-time to put daylight between the sides.
Winger Jordan Edmunds and centre Mark Hare the beneficiaries of two well-crafted Boroughmuir moves, the second featuring a strong involvement from ex-Red Rodger.
Half-time: Haddington 7-22 Boroughmuir
The Meggetland-based club showed why they've flown to the top of RBS National League with some ferocious defending, but the Reds didn't lie down - Alex Spence among those impressing for the hosts.
However, from turnover ball, the Reds were in danger again shortly after the break, as the visitors broke and full-back Craig Marshall grabbed the first of his brace.
His second came with 10 minutes to play, as he picked the perfect angle off a Muir lineout to score and seal victory for the visitors.
Kyle Adams crossed twice late on, the first after superb work from the pack allowed Herkes free, and he supplied the scoring pass to put the young winger in at the corner.
As the Reds pushed, Adams scored again after Ferguson broke the Muir line and out-stripping the covering defence to score under the posts from half-way. Ferguson again converted to make it 32-19.
Head coach Bryan Craig admitted he was hugely proud of his players’ efforts.
He said: "It was a huge defensive effort by all the boys – Garry Cockburn led from the front and put in another faultless performance
"Ice (Mamea) and Herkes were superb in the centre and Spence was imperious at openside.
“The boys can take great confidence from the fact they scored three tries against a team of this quality.”
The Reds now regroup and restart their league campaign with another home test, as they look to avenge the early season defeat to Livingston when they make the trip along the M8.