The compensation is the highest ever known to have been recovered from a religious body in Scotland.
The victims were preyed on by paedophile Ian Samson at Lord and Lady Polwarth Children’s House.
The siblings, who cannot be named for legal reasons, were repeatedly assaulted by the predator during a campaign of sexual and physical abuse that spanned three decades.
The girl was forced to endure an abortion when she became pregnant as a result of being raped.
Samson was jailed for 14 years in 2013 for 22 sex offences against eight children at the home, including rape.
The woman has now secured £500,000, the biggest publicly known payout to a child sex abuse survivor in Scotland.
Her brothers each received £250,000 after raising a civil case against the Kirk.
The siblings have welcomed the award but say their decision to mount legal action was about forcing the church to “do the right thing” and take responsibility for what happened under its charge.
“Samson was evil and robbed us of our childhood and our future,” they said in a statement.
“Our case has never been about the money – raising a civil action in the courts was the only way we could get any sort of acknowledgement from the Church of Scotland.
“It’s a shame that an organisation which promotes goodness and morals can’t do the right thing themselves and hold their hands up and apologise rather than force victims to endure further legal proceedings.
“We nearly gave up so many times in getting the Kirk to accept responsibility, so we’re delighted this is now over and have the justice and closure we need to get on with life as best we can.”
They encouraged anyone else affected by abuse to “be strong and step forward”.
Samson worked as a superintendent at the Lord and Lady Polwarth home alongside his wife, who was a matron there.
His vile campaign of abuse was carried out between the 1970s and 1990s and he used ice cream and the promise of cigarettes to target his victim.
Some children hid in cupboards or dog baskets to avoid being targeted and those who couldn’t escape were subjected to violent attacks – both physical and sexual.
The caretaker managed to keep his job at the care home despite being suspected of taking obscene photos of a child.
Eight of the offences took place at the home with others occurring at various locations across Edinburgh and the Lothians.
Specialist abuse lawyer Kim Leslie, a partner at Digby Brown Solicitors, who led the civil action against the church, said: “Ian Samson was rightly jailed for abuse he inflicted upon children after exploiting his position with the Church of Scotland. The significant sum secured for our clients also gives you an idea of how horrifically our clients suffered.”
The Kirk admitted it had failed the children, adding: “It felt important to us that there was full acknowledgment of the harm which did occur in our care at the time, and the longer term consequences for three siblings involved.”