But she expressed concern that there was no acceptable way to make that payment without disclosing it to the wider market.
Ms Baker was asked to see if there were any options or opportunities to structure the deal differently but there was no proposal that she could find that allowed her to do it, according to Mr Brown.
Mr Brown told jurors that Ms Baker had said that the advisory services agreement was essentially a mask for secretly paying the commission of 3.25 per cent but she believed her concerns had been escalated to the board.
Mr Brown said: "She was reassured that the board of Barclays had seen the information, had considered all the facts and had reached a decision on that basis to enter into the agreement.
"She was misled in this regard."
Mr Brown told how the advisory agreement was extremely vague about the services and did not include any kind of description of them.
Varley, of Notting Hill, Jenkins, of Malibu, California, Kalaris, of Knightsbridge, and Boath, of Henley-on-Thames, Oxfordshire, deny fraud by false representation, between 1 May 2008 and 31 August 2008.
Varley and Jenkins deny a second like charge of fraud by false representation, between 1 September 2008 and 30 November 2008.
The trial continues.