On Monday, winding up orders were made against the Thomas Cook Group and associated companies, making the future of the charity uncertain because it relies on the business for its income.
Callers to the telephone number listed on the charity’s website are played an automated message saying Thomas Cook has gone into liquidation.
"Thomas Cook UK plc and associated UK entities have entered compulsory liquidation and are now under the control of the Official Receiver," the message says.
"The UK business has ceased trading with immediate effect and all future flights and holidays are cancelled."
A spokesman for the Insolvency Service said the TCCC was an independent registered charity and was not involved in the current liquidation proceedings.
He said special managers from Alix Partners, which is handling the liquidation of the Thomas Cook airline and tour operator companies, were working to identify charity monies, "which will be passed on to the trustees of the charity in due course".
He said any questions about the future of the charity should be directed to its trustees.
A spokeswoman for the charity said it was preparing a statement.
A spokeswoman for the Charity Commission said: "According to our records, the Thomas Cook Children’s Charity has not contacted us in relation to the collapse of Thomas Cook.
"We will be contacting the trustees to seek information about how they are managing any risks to the charity and its beneficiaries."
The charity, which was registered with the commission in 2002, gave grants to charities and voluntary groups totalling £3m in the three years to the end of 2017, accounts show.
Its latest annual accounts, for 2017, say it had three main income streams: donations from Thomas Cook customers, the collection of unwanted foreign currency and funds raised by Thomas Cook employees.
The accounts say the company also provides "significant logistical support for the management and administrative functions that are required by the charity".
They say the founder of the trust was MyTravel Group, a company within the Thomas Cook group, which can remove trustees from the charity.
MyTravel Group is one of the companies that is being wound up as part of the liquidation proceedings.