The appointment runs counter to recent speculation that Premier Foods was considering selling off Mr Kipling after reports it had turned down an offer from United Biscuits.
Wilson, who will be responsible for Premier's cakes, desserts, home baking, spreads and beverages divisions, said he was confident the company could master the tough economic climate.
"We have seen high input costs, recessions and changes to VAT rates before," he said. "But we have also seen how winning businesses emerge from such times.
"It is about making sure your brand is offering better value across every dimension; and eliminating unnecessary costs."
"I see exciting times ahead over the coming months for the business and its people," he added.
"I want to make sure I use Premier's recent trading momentum to accelerate our brand equity and innovation programmes to lead growth in our categories and increase our market share."
Wilson will report to Will Carter, Premier's managing director for ambient, who said Wilson would add "immense value" to the business thanks to his experience in leading brand development.
Wilson was vice president of Kraft Foods' EU biscuits operation and had been with the company for 14 years. He replaces Jill Caseberry, who is leaving Premier at Christmas.