The teenager was in the 12th floor stairwell of the car park in Oswald Street, Glasgow, when the attack happened.
She was with a 17-year-old boy at the time.
Police appealed for information about the incident, which happened at about 11am on Tuesday July 29.
They are particularly keen to trace two people who were in the staircase at around that time and may be able to help with the inquiry.
A dark-haired woman carrying a quantity of books was seen entering the landing just before the 16-year-old was assaulted.
Shortly after the incident, a man with dark hair and wearing a dark suit passed them on the stairwell.
Detective Inspector Craig Willison of Greater Glasgow Division's CID, said: "We are keen to trace these two witnesses, who potentially could provide us with information which may help with our enquiry.
"I'd like to reassure the public that we are following a positive line of enquiry in this case and I would like to reiterate that Police Scotland takes any report of any sexual assault very seriously.
"If you are a victim, please contact us and we will provide you with the support you need."