Police said the boy has been charged with aggravated assault and aggravated sexual assault.
The girl, who is also 15, remains in critical condition as a result of the attack, which happened on Hargrave Street. She was found early Wednesday morning.
Const. Chris Wingfield with the Winnipeg Police Service said he doesn't know if the girl will survive.
He said the suspect and victim were known to each other.
"It's my understanding that they were walking around together downtown and some kind of argument ensued between the two of them."
Both the girl and the boy are in care of the province's Child and Family Services (CFS) system and were being housed at the same hotel not far from where the girl was found, police said.
The boy, who is now in custody at the Manitoba Youth Centre, was the one who flagged officers down for help, claiming to be a passerby who found the girl.
After questioning him, officers became suspicious of his story and pressed him further, which led to the arrest.
No other charges are expected, although the boy's charges would be upgraded if the girl does not survive, police said.
CBC News has talked to another teen who met the victim Tuesday evening and said she appeared to have been drinking and was with a group of friends when she left her hotel.
Tina Fontaine had been staying in same hotel
Last fall, CBC News did a series of stories about the troubles of teens in government care staying in hotels.
That followed the death in August of Tina Fontaine, another 15-year-old girl who was in CFS care and had been staying in the same downtown hotel as Wednesday's beating victim.
Fontaine's body was pulled from the Red River on Aug. 17, wrapped in a bag.
A week earlier, Fontaine was taken to hospital by ambulance after she was found passed out in a back lane. She was later returned to the hotel but was allowed to leave once again. She was reported missing the next day and not seen again until her body was found.
Police are treating her death as a homicide, but no arrests have been made to date.
Hours after news of the assault on Wednesday, Manitoba's Family Services Minister Kerri Irvin-Ross vowed, through tears and sobs, to end the practice of placing children in care in hotels by June 1.
Manitoba has about 10,000 children in care and on any given day, dozens are put up in hotel rooms because there aren't enough foster care homes.