The victim, known as AB, was sexually assaulted and beaten by Brothers Ryan, Farrell and Kelly at St Ninian’s School in Falkland, Fife.
The Christian Brothers, a religious sect that ran the school, tried to have the case thrown out but a sheriff ordered them to pay the damages.
AB now hopes his landmark victory will inspire others in their quest for justice.
He said: “Finally, after nearly 40 years, I’ve been acknowledged and those responsible can be exposed.”
AB was sent to St Ninian’s in February 1980 when he was 12-years-old and stayed there until April 1981.
He was raped, molested and beaten by all three Brothers and even forced to watch attacks on other children.
Kelly, Farrell and Ryan commonly targeted children in a dormitory they referred to as “the favourite boys room”.
AB, who is now 54-years-old, kept his past secret until November 2013 when he spoke to police officers.
He said: “I just broke down in tears. Until then I’d been living in my head for 30 years.
“It was terrifying but empowering. Exhausting but freeing. Painful but therapeutic.”
In July 2016, Brother Farrell was convicted of four abuse charges and Brother Kelly was convicted of six charges at the High Court in Glasgow
Farrell was jailed for five years and Kelly for 10 years. Brother Ryan died before he could be investigated.
AB’s evidence did not play a part in the convictions but this month a sheriff ruled the abuse did occur due to the volume of supporting evidence gathered during a historic abuse claim with legal firm Digby Brown.
The Christian Brothers tried to have the civil action thrown out as the death of Brother Ryan meant they couldn’t investigate AB’s allegations.
But Sheriff Christopher Dickson dismissed this argument and ordered them to pay AB £1.39m in damages in recognition of the lifelong impact.
In his 173-page judgment, Sheriff Dickson said: “I did not consider that the death of one of three alleged abusers automatically resulted in the defender proving substantial prejudice in so far as the case is directed against Brother Ryan.
“The pursuer’s psychiatric conditions have prevented him from working for the past 38 years. I find that the defender is liable to make reparation to the pursuer.”
Following the ruling, AB said: “I’ll always feel the pain. I’ll always have flashbacks.
“But at least now I’m not alone. I am supported. I have been recognised. And I can now slowly look to the future instead of being chained to my past.”
Kim Leslie, Partner at Digby Brown, led the legal fight that helped AB secure the landmark victory.
She said: “Firstly, I’d like to pay tribute to AB for speaking out then staying steadfast as he took on a religious organisation - it makes this ruling all the more poignant.
“No amount of compensation or redress can alter the past but it can help improve a person’s future – but just as importantly, cases like these hold those responsible to account which in turn improves access to justice for others.”