Elaine McGonigle, 48, of Errol, Perthshire, has been accused of the fraud while at the Royal Hospital for Sick Children in Edinburgh.
McGonigle was excused attending Edinburgh Sheriff Court yesterday as the hearing was for a legal debate on a defence motion.
Her solicitor, Peter Robertson, told Sheriff Nigel Morrison, QC, he was withdrawing the motion and that his client was now pleading not guilty to all charges.
Fiscal Depute Aidan Higgins said the trial was "likely to take some time" and it was fixed for three days in May next year.
It is alleged that between September 2008 and March 2010, while she was the fundraising director of New Pyjamas, McGonigle defrauded the charity of £1855.
The allegations include a claim for £436.38 in fares for business flights to London when the sum was instead spent on a flight to Majorca for herself, husband and son.