The news comes on the same day as Irish striker Stephen O'Flynn completed his move to Northampton, having been out of contract with Limerick of Ireland.
19-year-old centre-half Wilkinson is described by manager Ian Sampson on the official club website as a 'confident lad' who will add to competition for places among the Cobblers rearguard.
A third deal, for former Coventry City midfielder Kevin Thornton, remains on the table as Sampson shuffles his pack for the second-half of the season.