Billy Lumley will deputise in goal, having made his debut for the Cobblers in the 3-2 defeat to Crewe Alexandra.
Manager Ian Sampson told BBC Radio Northampton: "He had an operation [on Saturday] on cartilage in his knee.
"We're going to lose him, hopefully for just three weeks. Billy is a confident boy, he's our number two goalkeeper so he deserves a chance."
Former Wolves keeper Lumley, 20, signed for Northampton from the Glenn Hoddle Academy in December. 2009.
Source: BBC Sport
Source: BBC Sport