Mr. Thomas becomes executive chairman of NTFC and his first task was to pay £166,000 to HMRC who will now withdraw their winding-up petition.
Friday's adjournment petition brought by Northampton Borough Council, as part of their efforts to find a solution to the crisis, is set to be adjourned after an agreement was reached between Mr. Thomas and the council over the £10.25m loan payment previously made to the club.
Overdue staff wage payments from October are set to be made next week.
"We have the funds in place to take care of the short and long-term needs of the club which has been shown to both the council and the Football League, and we will be working hard over the next few months to understand the areas of investment required and then implement plans accordingly," said Mr. Thomas in a statement.