David James Leblanc was arrested Sunday night on a logging trail near Longlac, Ont., about 260 kilometres northeast of Thunder Bay.
He was taken into custody, but until now, police said, for "medical reasons" he wasn't fit to fly.
He arrived in an RCMP plane after 6 p.m. AT.
Leblanc's feet were wrapped in bandages and he had trouble walking down the plane's stairs, reported the CBC's Brian DuBreuil.
He will appear in court in Bridgewater, N.S., on Tuesday morning. Leblanc has been charged with forcible confinement and sexual assault in the case of a teenager who was allegedly kept at a house on Nova Scotia's South Shore for two weeks.
The body of the other suspect, Wayne Alan Cunningham, was found Wednesday night, not far from where Leblanc was arrested, effectively ending a national manhunt for the two men, which started last week after the teenager escaped from the house and walked more than one kilometre to a home seeking help.
An arrest warrant for the Leblanc and Cunningham read, "Over the course of several days these two men forcibly confined and sexually assaulted [the teen]," and that the two "were talking about trying to sell him."
The teen had chains wrapped around his wrists and ankles and was wearing nothing but a hooded sweatshirt and a hat when he arrived on Terry Frauzel's doorstep.
Frauzel told CBC News he cut the chains off the boy and drove him to a house in Bridgewater.
The teen was later treated in hospital, and police say he is now safe.