The 14-year-old had been going to the toilets in the Arndale Centre, near the entrance of Aldi and Subway, when he was approached by the men.
After threatening the boy, they led him to a nearby Debenhams, where one of them assaulted him in a toilet.
Greater Manchester Police (GMP) has released CCTV of two men they want to trace after the attack on 2 June.
Police said one of the attackers was Asian and one white.
The victim was told by one of the men: "Come with us, do what we say and if you try to run we'll get you."
GMP said he had been grabbed by the arm, led out of the Arndale Centre and taken to Debenhams at about 17:45 BST.
Supt Stuart Ellison, of Greater Manchester Police, said the boy was "traumatised"
He was taken upstairs in the lift and marched to a toilet where he was raped by the Asian man.
GMP said the traumatised victim had contacted police after the assault and had been supported by specially trained officers.
Those officers have spent the past two months working with the boy to build up a picture of what happened and have been waiting for forensic results before deciding to issue an appeal, a spokesman said.
Supt Stuart Ellison said: "When you think about a 14-year-old out in the city centre at that time of the evening, when the footfall is pretty heavy and there are a lot of people about, the fact that someone could be marched across the street and into a store in this way is pretty horrific."
He added that he found the attack "particularly disturbing" and said: "When I think about family or friends who could have been out in the Arndale at that time of night, it disturbs me greatly."
Det Sgt Liam Boden, of North Manchester CID, added: "This young victim has been absolutely devastated by what happened to him.
"I am confident that shoppers may have seen the offenders either before or after the incident.
"I want people to take a good look at the men in these images and tell me who they are."
A Debenhams spokeswoman said: "We were shocked to hear about this incident and would like to reassure everyone this is an isolated case."
She said that following the assault the store had carried out regular toilet checks and briefed the cleaners to report any suspicious activity as well as putting the camera of the entrance to the toilets on a permanent monitor in the CCTV control room.
Anyone with information is asked to call North Manchester CID or Crimestoppers.
Ugh. Why do people do these things?