The company’s group chief executive Peter Fankhauser confirmed it had received the sum from the owners of the Louis Corcyra Beach Hotel on the Greek holiday island of Corfu, where Bobby and Christi Shepherd died.
Mr Fankhauser said: “I believe this is the right thing to do and I apologise to the family for all they have gone through.”
Bobby and Christi, aged six and seven, died when they were overcome by fumes from a faulty boiler as they stayed in a bungalow in the grounds of the hotel with their father, Neil Shepherd and his partner, now wife, Ruth, in October 2006.
Last week, an inquest jury concluded that Thomas Cook breached its duty of care to the family and returned verdicts of unlawful killing.
Since then, Mr Shepherd and the children’s mother, Sharon Wood, have criticised Thomas Cook for failing to apologise.
Yesterday, Mr Fankhauser confirmed that his firm received the £1.5m, mainly in respect of legal fees, as part of a £3m settlement with Louis Group, the hotel owners.
The other £1.5m went to Thomas Cook’s insurers.
Mr Fankhauser said: “Thomas Cook has not in any way profited from our claim against the hotel owner. In late 2012, we brought a claim against the hotelier for breaching their contract to provide safe accommodation to our customers and to comply with all applicable laws, which was decided in our favour.
“Today I have made arrangements for the full amount – £1.5m – to be donated in full to Unicef, the world’s leading children’s organisation.”
The move by Thomas Cook follows criticism of the firm from the parents of Bobby and Christi over the weekend.
On Wednesday, a jury at the inquests concluded the firm had “breached their duty of care” to the family and outlined a series of failings by the tour company.
After the end of the two-week inquest hearing in Wakefield, Mrs Wood said: “I will always hold Thomas Cook responsible for their deaths.”
The family’s barrister Leslie Thomas QC said the firm should “hang its head in shame”.
The hearing heard that Bobby and Christi, from Horbury, near Wakefield, died due to multiple flaws in the installation and maintenance of the hot water boiler in an outbuilding next to the bungalow where they were staying on a half-term break.
Mr and Mrs Shepherd were with Christi and Bobby when the tragedy happened and were found unconscious next to the two dead children.
Two Thomas Cook employees were tried in a Greek court for manslaughter but were cleared five years ago.
Four Greek nationals were convicted of offences relating to the deaths of the children and jailed but were released pending appeal hearings.
Mr Fankhauser previously said Thomas Cook had nothing to apologise for and announced the charity cash move after the payment to the firm was exposed at the weekend, sparking a storm of condemnation.