The two youths are being questioned at Letterkenny Garda Station.
The incident is believed to have taken place at around 10pm at the carpark at the back of Mr Chippie and O’Boyces Corner close to the Port Roundabout.
The area was sealed of as investigators carried out a search of the area.
While Gardai would not go into details regarding the nature of the assault, they have said it is a very sensitive matter.
Garda forensic officers carried out a full investigation as the area of the alleged assault was cordoned off throughout Saturday afternoon.
Gardai are asking anyone who was in the area at the time and may have witnessed anything to contact Letterkenny Gardai.
Two other juveniles who were arrested on Saturday were released that evening.