Nicholls has undergone two operations after suffering a double leg fracture following a late tackle from Port Vale's John McCombe on Saturday.
"We are probably looking at six to nine months for him," PA Sport quotes Boothroyd as saying. "He's had a skin graft and his shin is pinned so that is going to be a long job.
"He's very down at the moment, as you can imagine, but he's had lots of goodwill messages from supporters and he's asked me to pass on his thanks for that.
"I'd also like to thank all those people around the club who acted so quickly on Saturday to get Alex sorted and into hospital, including the club doctor, Stuart Barker the physio and all the St John's ambulance people and the paramedics."
Nicholls joined Northampton from Walsall in July and has scored seven goals in his first 15 starts.