Prince Philip called at the Doncaster branch of the roadside restaurant chain, which is on the A1, just north of the South Yorkshire town, with security guards and other staff.
Manager Celia Morrell said one of her staff asked him if wanted a table but he politely refused, saying he just wanted to stretch his legs as his staff bought take-away coffee and snacks.
Ms Morrell, 52, said the restaurant was busy and she did not realise who it was at first - and neither did her young colleague.
"It was really exciting and also an honour that they'd picked our Little Chef to come and visit," she said.
"There was quite a large group of them and they were in the takeaway area. Prince Philip was wandering around and one of the girls went up and asked him if he would like a table. She's only a young girl and she didn't realise who he was.
"He said 'Oh no, I'm just stretching my legs' and he wandered around a bit more.
"The security people were buying drinks and chocolates."
Ms Morrell said the worker who spoke to him did not spot who their VIP guest was until she returned.
"I said to her 'do you realise who that was?' and she was amazed when I told her."