The girl, aged 14, told police she was assaulted in the area near the Beachcomber pub at the junction of Marine Parade and Dane Road, at about 10pm on Friday.
Police have not disclosed whether the incident occurred on the promenade or beach, or elsewhere.
Police say the victim was in a 'very distressed state' and walked to public toilets at the corner of Place Lane, where she was helped by a man and a woman.
A police spokesman said they needed to speak to the couple and to anyone else who may have spoken to the victim in the area at around the same time.
The 16-year-old boy arrested on suspicion of rape has been released on police bail pending further inquiries.
Anyone with information should call Sussex Police on 0845 60 70 999, quoting serial 2303 of August 8.
A spokesman for Newhaven CID said, "Information we have to date is that there is no indication that this was a stranger attack."