The 24-year-old suffered a hamstring strain in the 1-0 defeat to Bradford City at the weekend, with Boothroyd revealing that "it will probably be a fairly long one".
"I think that will be his season over. We don't really know at this stage but it will probably be a fairly long one," Bothroyd told reporters following the match.
"It's that stage of the season where you get these things. He's done well for us recently and it will be a blow. But it will give Jake Robinson the chance to have a run in the side and show us what he can do."
Northampton currently sit third in the League Two table.